Packages [R]

GNU Guix provides 6,344 packages transparently available as pre-built binaries. These pages provide a complete list of the packages. Our continuous integration system shows their current build status (updated October 17, 2017).

You can browse packages indexed by their first letter.

GNU?Package versionPackage details
Part of GNU r 3.4.2 Environment for statistical computing and graphics

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.

http://www.r-project.org/
r-acepack 1.4.1 Functions for regression transformations

This package provides ACE and AVAS methods for choosing regression transformations.

http://cran.r-project.org/web/packages/acepack
r-acsnminer 0.16.8.25 Gene enrichment analysis

This package provides tools to compute and represent gene set enrichment or depletion from your data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN) or user imported maps. The gene set enrichment can be run with hypergeometric test or Fisher exact test, and can use multiple corrections. Visualization of data can be done either by barplots or heatmaps.

http://cran.r-project.org/web/packages/ACSNMineR
r-adaptivesparsity 1.4 Adaptive sparsity models

This package implements the Figueiredo machine learning algorithm for adaptive sparsity and the Wong algorithm for adaptively sparse gaussian geometric models.

http://cran.r-project.org/web/packages/AdaptiveSparsity
r-ade4 1.7-8 Multivariate data analysis and graphical display

The ade4 package contains data analysis functions to analyze ecological and environmental data in the framework of Euclidean exploratory methods.

http://pbil.univ-lyon1.fr/ADE-4
r-affy 1.54.0 Methods for affymetrix oligonucleotide arrays

This package contains functions for exploratory oligonucleotide array analysis.

http://bioconductor.org/packages/affy
r-affyio 1.46.0 Tools for parsing Affymetrix data files

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

https://github.com/bmbolstad/affyio
r-annotate 1.54.0 Annotation for microarrays

This package provides R environments for the annotation of microarrays.

http://bioconductor.org/packages/annotate
r-annotationdbi 1.38.2 Annotation database interface

This package provides user interface and database connection code for annotation data packages using SQLite data storage.

http://bioconductor.org/packages/AnnotationDbi
r-annotationfilter 1.0.0 Facilities for filtering Bioconductor annotation resources

This package provides classes and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters are used by ensembldb, Organism.dplyr, and other packages.

https://github.com/Bioconductor/AnnotationFilter
r-annotationforge 1.18.1 Code for building annotation database packages

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

http://bioconductor.org/packages/AnnotationForge
r-annotationhub 2.8.2 Client to access AnnotationHub resources

This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g. VCF, bed, wig) and other resources from standard locations (e.g. UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.

http://bioconductor.org/packages/AnnotationHub
r-ape 4.1 Analyses of phylogenetics and evolution

This package provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, and several other tools.

http://ape-package.ird.fr/
r-aroma-light 3.6.0 Methods for normalization and visualization of microarray data

This package provides methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

https://github.com/HenrikBengtsson/aroma.light
r-assertthat 0.2.0 Easy pre and post assertions

Assertthat is an extension to stopifnot() that makes it easy to declare the pre and post conditions that your code should satisfy, while also producing friendly error messages so that your users know what they've done wrong.

https://github.com/hadley/assertthat
r-auc 0.3.0 Compute the area under the curve of selected measures

This package includes functions to compute the area under the curve of selected measures: the area under the sensitivity curve (AUSEC), the area under the specificity curve (AUSPC), the area under the accuracy curve (AUACC), and the area under the receiver operating characteristic curve (AUROC). The curves can also be visualized. Support for partial areas is provided.

http://cran.r-project.org/web/packages/AUC
r-backports 1.1.1 Reimplementations of functions introduced since R 3.0.0

Provides implementations of functions which have been introduced in R since version 3.0.0. The backports are conditionally exported which results in R resolving the function names to the version shipped with R (if available) and uses the implemented backports as fallback. This way package developers can make use of the new functions without worrying about the minimum required R version.

http://cran.r-project.org/web/packages/backports
r-bamsignals 1.8.0 Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of nucleotide sequence reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

http://bioconductor.org/packages/bamsignals
r-base64 2.0 Base64 encoder and decoder

This package is a compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the openssl or base64enc package instead.

http://cran.r-project.org/web/packages/base64
r-base64enc 0.1-3 Tools for Base64 encoding

This package provides tools for handling Base64 encoding. It is more flexible than the orphaned "base64" package.

http://www.rforge.net/base64enc
r-batchjobs 1.6 Batch computing with R

This package provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine. Multicore and SSH systems are also supported.

https://github.com/tudo-r/BatchJobs
r-bbmisc 1.11 Miscellaneous functions for R package development

This package provides miscellaneous helper functions for the development of R packages.

https://github.com/berndbischl/BBmisc
r-bbmle 1.0.19 Tools for General Maximum Likelihood Estimation

Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the mle classes in the stats4 package.

http://cran.r-project.org/web/packages/bbmle
r-beeswarm 0.2.3 Implementation of bee swarm plots

This package provides an implementation of bee swarm plots. The bee swarm plot is a one-dimensional scatter plot like stripchart, but with closely-packed, non-overlapping points.

http://www.cbs.dtu.dk/~eklund/beeswarm/
r-bh 1.65.0-1 R package providing subset of Boost headers

This package aims to provide the most useful subset of Boost libraries for template use among CRAN packages.

https://github.com/eddelbuettel/bh
r-biased-urn 1.07 Biased urn model distributions

This package provides statistical models of biased sampling in the form of univariate and multivariate noncentral hypergeometric distributions, including Wallenius' noncentral hypergeometric distribution and Fisher's noncentral hypergeometric distribution (also called extended hypergeometric distribution).

http://www.agner.org/random/
r-bigmemory 4.5.19 Manage large matrices with shared memory or memory-mapped files

This package provides methods to create, store, access, and manipulate large matrices. Matrices are allocated to shared memory and may use memory-mapped files.

http://www.bigmemory.org
r-bigmemory-sri 0.1.3 Shared resource interface for the bigmemory package

This package provides a shared resource interface for the bigmemory and synchronicity packages.

http://cran.r-project.org/web/packages/bigmemory.sri
r-bindr 0.1 Parametrized active bindings

This package provides a simple interface for creating active bindings where the bound function accepts additional arguments.

https://github.com/krlmlr/bindr
r-bindrcpp 0.2 Rcpp interface to active bindings

This package provides an easy way to fill an environment with active bindings that call a C++ function.

https://github.com/krlmlr/bindrcpp
r-biobase 2.36.2 Base functions for Bioconductor

This package provides functions that are needed by many other packages on Bioconductor or which replace R functions.

http://bioconductor.org/packages/Biobase
r-bioccheck 1.12.0 Executes Bioconductor-specific package checks

This package contains tools to perform additional quality checks on R packages that are to be submitted to the Bioconductor repository.

http://bioconductor.org/packages/BiocCheck
r-biocgenerics 0.22.0 S4 generic functions for Bioconductor

This package provides S4 generic functions needed by many Bioconductor packages.

http://bioconductor.org/packages/BiocGenerics
r-biocinstaller 1.26.0 Install Bioconductor packages

This package is used to install and update R packages from Bioconductor, CRAN, and Github.

http://bioconductor.org/packages/BiocInstaller
r-biocparallel 1.10.1 Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

http://bioconductor.org/packages/BiocParallel
r-biocstyle 2.4.1 Bioconductor formatting styles

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

http://bioconductor.org/packages/BiocStyle
r-biocviews 1.44.0 Bioconductor package categorization helper

The purpose of biocViews is to create HTML pages that categorize packages in a Bioconductor package repository according to keywords, also known as views, in a controlled vocabulary.

http://bioconductor.org/packages/biocViews
r-biomart 2.32.1 Interface to BioMart databases

biomaRt provides an interface to a growing collection of databases implementing the http://www.biomart.org. The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

http://bioconductor.org/packages/biomaRt
r-biostrings 2.44.2 String objects and algorithms for biological sequences

This package provides memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

http://bioconductor.org/packages/Biostrings
r-bit 1.1-12 Class for vectors of 1-bit booleans

This package provides bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts, fast boolean operators and fast summary statistics. With bit class vectors of true binary booleans, TRUE and FALSE can be stored with 1 bit only.

http://ff.r-forge.r-project.org
r-bit64 0.9-7 S3 class for vectors of 64 bit integers

The bit64 package provides serializable S3 atomic 64 bit (signed) integers that can be used in vectors, matrices, arrays and data.frames. Methods are available for coercion from and to logicals, integers, doubles, characters and factors as well as many elementwise and summary functions. Many fast algorithmic operations such as match and order support interactive data exploration and manipulation and optionally leverage caching.

http://ff.r-forge.r-project.org/
r-bitops 1.0-6 Bitwise operations

This package provides functions for bitwise operations on integer vectors.

http://cran.r-project.org/web/packages/bitops
r-blob 1.1.0 Simple S3 Class for representing vectors of binary data

Raw vectors in R are useful for storing a single binary object. What if you want to put a vector of them in a data frame? The blob package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.

https://github.com/hadley/blob
r-bookdown 0.5 Authoring books and technical documents with R markdown

This package provides output formats and utilities for authoring books and technical documents with R Markdown.

https://github.com/rstudio/bookdown
r-boot 1.3-20 Bootstrap functions for R

This package provides functions and datasets for bootstrapping from the book "Bootstrap Methods and Their Application" by A.C. Davison and D.V. Hinkley (1997, CUP), originally written by Angelo Canty for S.

non-copyleft (This is a lax, non-copyleft free software license. Check the URI for details. )
http://cran.r-project.org/web/packages/boot
r-brew 1.0-6 Templating framework for report generation

The brew package implements a templating framework for mixing text and R code for report generation. The template syntax is similar to PHP, Ruby's erb module, Java Server Pages, and Python's psp module.

http://cran.r-project.org/web/packages/brew
r-bsgenome 1.44.0 Infrastructure for Biostrings-based genome data packages

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation.

http://bioconductor.org/packages/BSgenome
r-bsgenome-celegans-ucsc-ce10 1.4.0 Full genome sequences for Worm

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/
r-bsgenome-celegans-ucsc-ce6 1.4.0 Full genome sequences for Worm

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/
r-bsgenome-dmelanogaster-ucsc-dm3 1.4.0 Full genome sequences for Fly

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/
r-bsgenome-hsapiens-1000genomes-hs37d5 0.99.1 Full genome sequences for Homo sapiens

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.

http://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/
r-bsgenome-hsapiens-ucsc-hg19 1.4.0 Full genome sequences for Homo sapiens

This package provides full genome sequences for Homo sapiens as provided by UCSC (hg19, February 2009) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/
r-bsgenome-mmusculus-ucsc-mm10 1.4.0 Full genome sequences for Mouse

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/
r-bsgenome-mmusculus-ucsc-mm9 1.4.0 Full genome sequences for Mouse

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects.

http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/
r-cairo 1.5-9 R graphics device using Cairo graphics library

This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.

http://www.rforge.net/Cairo/
r-calibrate 1.7.2 Calibration of scatterplot and biplot axes

This is a package for drawing calibrated scales with tick marks on (non-orthogonal) variable vectors in scatterplots and biplots.

http://cran.r-project.org/web/packages/calibrate
r-car 2.1-5 Companion to applied regression

This package provides functions and datasets from book Companion to Applied regression, Second Edition, Sage, 2011.

https://r-forge.r-project.org/projects/car/
r-caret 6.0-77 Classification and regression training

This package provides misc functions for training and plotting classification and regression models.

https://github.com/topepo/caret
r-category 2.42.1 Category analysis

This package provides a collection of tools for performing category analysis.

http://bioconductor.org/packages/Category
r-catools 1.17.1 Various tools including functions for moving window statistics

This package contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.

http://cran.r-project.org/web/packages/caTools
r-cellranger 1.1.0 Translate spreadsheet cell ranges to rows and columns

This package provides helper functions to work with spreadsheets and the A1:D10 style of cell range specification.

https://github.com/rsheets/cellranger
r-centipede 1.2 Predict transcription factor binding sites

CENTIPEDE applies a hierarchical Bayesian mixture model to infer regions of the genome that are bound by particular transcription factors. It starts by identifying a set of candidate binding sites, and then aims to classify the sites according to whether each site is bound or not bound by a transcription factor. CENTIPEDE is an unsupervised learning algorithm that discriminates between two different types of motif instances using as much relevant information as possible.

http://centipede.uchicago.edu/
r-checkmate 1.8.4 Fast and versatile argument checks

This package provides tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.

https://github.com/mllg/checkmate
r-chipkernels 1.1-1.c9cfcacb6 Build string kernels for DNA Sequence analysis

ChIPKernels is an R package for building different string kernels used for DNA Sequence analysis. A dictionary of the desired kernel must be built and this dictionary can be used for determining kernels for DNA Sequences.

https://github.com/ManuSetty/ChIPKernels
r-chipseq 1.26.0 Package for analyzing ChIPseq data

This package provides tools for processing short read data from ChIPseq experiments.

http://bioconductor.org/packages/chipseq
r-chron 2.3-50 Chronological R objects which can handle dates and times

This package provides chronological R objects which can handle dates and times.

http://cran.r-project.org/web/packages/chron
r-circlize 0.4.1 Circular visualization

Circular layout is an efficient way for the visualization of huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. The flexibility of the package is based on the usage of low-level graphics functions such that self-defined high-level graphics can be easily implemented by users for specific purposes. Together with the seamless connection between the powerful computational and visual environment in R, it gives users more convenience and freedom to design figures for better understanding complex patterns behind multiple dimensional data.

https://github.com/jokergoo/circlize
r-class 7.3-14 R functions for classification

This package provides various functions for classification, including k-nearest neighbour, Learning Vector Quantization and Self-Organizing Maps.

http://www.stats.ox.ac.uk/pub/MASS4/
r-cluster 2.0.6 Methods for data cluster analysis

This package provides tools that are useful in finding groups in data. It is based on the methods described in Kaufman and Rousseeuw (1990) "Finding Groups in Data".

http://cran.r-project.org/web/packages/cluster
r-coda 0.19-1 This is a package for Output Analysis and Diagnostics for MCMC

This package provides functions for summarizing and plotting the output from Markov Chain Monte Carlo (MCMC) simulations, as well as diagnostic tests of convergence to the equilibrium distribution of the Markov chain.

http://cran.r-project.org/web/packages/coda
r-codetools 0.2-15 Code analysis tools for R

This package provides code analysis tools for R to check R code for possible problems.

https://cran.r-project.org/web/packages/codetools
r-colorspace 1.3-2 Color space manipulation

This package carries out a mapping between assorted color spaces including RGB, HSV, HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB. Qualitative, sequential, and diverging color palettes based on HCL colors are provided.

http://cran.r-project.org/web/packages/colorspace
r-commonmark 1.4 CommonMark and Github Markdown Rendering in R

The CommonMark specification defines a rationalized version of markdown syntax. This package uses the 'cmark' reference implementation for converting markdown text into various formats including HTML, LaTeX and groff man. In addition, it exposes the markdown parse tree in XML format. The latest version of this package also adds support for Github extensions including tables, autolinks and strikethrough text.

http://cran.r-project.org/web/packages/commonmark
r-compare 0.2-6 Comparing objects for differences

This package provides functions to compare a model object to a comparison object. If the objects are not identical, the functions can be instructed to explore various modifications of the objects (e.g., sorting rows, dropping names) to see if the modified versions are identical.

http://cran.r-project.org/web/packages/compare
r-compquadform 1.4.3 Distribution function of quadratic forms in normal variables

This package provides functions to compute the distribution function of quadratic forms in normal variables using Imhof's method, Davies's algorithm, Farebrother's algorithm or Liu et al.'s algorithm.

http://cran.r-project.org/web/packages/CompQuadForm
r-copyhelper 1.6.0 Helper files for CopywriteR

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.

http://bioconductor.org/packages/CopyhelpeR/
r-copywriter 2.8.1 Copy number information from targeted sequencing

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

https://github.com/PeeperLab/CopywriteR
r-cowplot 0.8.0 Streamlined plot theme and plot annotations for ggplot2

This package provides some helpful extensions and modifications to the ggplot2 package to combine multiple ggplot2 plots into one and label them with letters, as is often required for scientific publications.

https://github.com/wilkelab/cowplot
r-crayon 1.3.4 Colored terminal output for R

Colored terminal output on terminals that support ANSI color and highlight codes. It also works in Emacs ESS. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the "chalk" JavaScript project.

https://github.com/gaborcsardi/crayon
r-crosstalk 1.0.0 Inter-widget interactivity for HTML widgets

This package provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). It currently supports linked brushing and filtering.

https://rstudio.github.io/crosstalk/
r-curl 2.8.1 HTTP client for R

The curl() and curl_download() functions provide highly configurable drop-in replacements for base url() and download.file() with better performance, support for encryption, gzip compression, authentication, and other libcurl goodies. The core of the package implements a framework for performing fully customized requests where data can be processed either in memory, on disk, or streaming via the callback or connection interfaces.

https://github.com/jeroenooms/curl
r-cvst 0.2-1 Fast cross-validation via sequential testing

This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.

http://cran.r-project.org/web/packages/CVST
r-data-table 1.10.4 Enhanced version of data.frame R object

The R package data.table is an extension of data.frame providing functions for fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group, column listing and fast file reading.

https://github.com/Rdatatable/data.table/wiki
r-dbi 0.7 R database interface

The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

https://github.com/rstats-db/DBI
r-dbplyr 1.1.0 Dplyr back end for databases

This package provides a dplyr back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a DBI back end; more advanced features require SQL translation to be provided by the package author.

https://github.com/tidyverse/dbplyr
r-ddalpha 1.3.1 Depth-Based classification and calculation of data depth

This package contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.

http://cran.r-project.org/web/packages/ddalpha
r-delayedarray 0.2.7 Delayed operations on array-like objects

Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.

http://bioconductor.org/packages/DelayedArray
r-dendextend 1.5.2 Extending 'dendrogram' functionality in R

This package offers a set of functions for extending dendrogram objects in R, letting you visualize and compare trees of hierarchical clusterings. You can adjust a tree's graphical parameters (the color, size, type, etc of its branches, nodes and labels) and visually and statistically compare different dendrograms to one another.

https://cran.r-project.org/web/packages/dendextend
r-deoptimr 1.0-8 Differential evolution optimization in pure R

This package provides a differential evolution (DE) stochastic algorithms for global optimization of problems with and without constraints. The aim is to curate a collection of its state-of-the-art variants that (1) do not sacrifice simplicity of design, (2) are essentially tuning-free, and (3) can be efficiently implemented directly in the R language.

http://cran.r-project.org/web/packages/DEoptimR
r-desc 1.1.1 Manipulate DESCRIPTION Files

This package provides tools to read, write, create, and manipulate DESCRIPTION files. It is intended for packages that create or manipulate other packages.

https://github.com/r-pkgs/desc
r-deseq 1.28.0 Differential gene expression analysis

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

http://www-huber.embl.de/users/anders/DESeq
r-deseq2 1.16.1 Differential gene expression analysis

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

http://bioconductor.org/packages/DESeq2
r-devtools 1.13.3 Tools to make developing R packages easier

The devtools package is a collection of package development tools to simplify the devolpment of R packages.

https://github.com/hadley/devtools
r-dexseq 1.22.0 Inference of differential exon usage in RNA-Seq

This package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.

http://bioconductor.org/packages/DEXSeq
r-dichromat 2.0-0 Color schemes for dichromats

Dichromat collapses red-green or green-blue distinctions to simulate the effects of different types of color-blindness.

http://cran.r-project.org/web/packages/dichromat
r-digest 0.6.12 Create cryptographic hash digests of R objects

This package contains an implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the md5, sha-1, sha-256, crc32, xxhash and murmurhash algorithms) permitting easy comparison of R language objects, as well as a function 'hmac()' to create hash-based message authentication code.

Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as OpenSSL should be used.

http://dirk.eddelbuettel.com/code/digest.html
r-dimred 0.1.0 Framework for dimensionality reduction

This package provides a collection of dimensionality reduction techniques from R packages and provides a common interface for calling the methods.

https://github.com/gdkrmr/dimRed
r-diptest 0.75-7 Hartigan's dip test statistic for unimodality

This package computes Hartigan's dip test statistic for unimodality, multimodality and provides a test with simulation based p-values, where the original public code has been corrected.

http://cran.r-project.org/web/packages/diptest
r-distillery 1.0-4 Functions for confidence intervals and object information

This package provides some very simple method functions for confidence interval calculation and to distill pertinent information from a potentially complex object; primarily used in common with the packages extRemes and SpatialVx.

http://www.ral.ucar.edu/staff/ericg
r-dnacopy 1.50.1 Implementation of a circular binary segmentation algorithm

This package implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

https://bioconductor.org/packages/DNAcopy
r-domc 1.3.4 Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the multicore functionality of the parallel package.

http://cran.r-project.org/web/packages/doMC
r-doparallel 1.0.11 Foreach parallel adaptor for the 'parallel' package

This package provides a parallel backend for the %dopar% function using the parallel package.

http://cran.r-project.org/web/packages/doParallel
r-dplyr 0.7.3 Tools for working with data frames in R

dplyr is the next iteration of plyr. It is focussed on tools for working with data frames. It has three main goals: 1) identify the most important data manipulation tools needed for data analysis and make them easy to use in R; 2) provide fast performance for in-memory data by writing key pieces of code in C++; 3) use the same code interface to work with data no matter where it is stored, whether in a data frame, a data table or database.

https://github.com/hadley/dplyr
r-drr 0.0.2 Dimensionality reduction via regression

This package provides an implementation of dimensionality reduction via regression using Kernel Ridge Regression.

http://cran.r-project.org/web/packages/DRR
r-dt 0.2 R wrapper of the DataTables JavaScript library

This package allows for data objects in R to be rendered as HTML tables using the JavaScript library 'DataTables' (typically via R Markdown or Shiny). The 'DataTables' library has been included in this R package.

http://rstudio.github.io/DT
r-dynamictreecut 1.63-1 Detect clusters in hierarchical clustering dendrograms

This package contains methods for the detection of clusters in hierarchical clustering dendrograms.

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/BranchCutting/
r-e1071 1.6-8 Miscellaneous functions for probability theory

This package provides functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, naive Bayes classifier, and more.

http://cran.r-project.org/web/packages/e1071
r-edaseq 2.10.0 Exploratory data analysis and normalization for RNA-Seq

This package provides support for numerical and graphical summaries of RNA-Seq genomic read data. Provided within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization. Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization.

https://github.com/drisso/EDASeq
r-edger 3.18.0 EdgeR does empirical analysis of digital gene expression data

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

http://bioinf.wehi.edu.au/edgeR
r-emdbook 1.3.9 Support functions and data for "Ecological Models and Data"

This package provides auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

http://www.math.mcmaster.ca/bolker/emdbook
r-energy 1.7-2 Multivariate inference via the energy of data

This package provides e-statistics (energy) tests and statistics for multivariate and univariate inference, including distance correlation, one-sample, two-sample, and multi-sample tests for comparing multivariate distributions, are implemented. Measuring and testing multivariate independence based on distance correlation, partial distance correlation, multivariate goodness-of-fit tests, clustering based on energy distance, testing for multivariate normality, distance components (disco) for non-parametric analysis of structured data, and other energy statistics/methods are implemented.

http://cran.r-project.org/web/packages/energy
r-estimability 1.2 Tools for assessing estimability of linear predictions

Provides tools for determining estimability of linear functions of regression coefficients, and 'epredict' methods that handle non-estimable cases correctly.

http://cran.r-project.org/web/packages/estimability
r-evaluate 0.10.1 Parsing and evaluation tools for R

This package provides tools that allow you to recreate the parsing, evaluation and display of R code, with enough information that you can accurately recreate what happens at the command line. The tools can easily be adapted for other output formats, such as HTML or LaTeX.

https://github.com/hadley/evaluate
r-extremes 2.0-8 Extreme value analysis

ExtRemes is a suite of functions for carrying out analyses on the extreme values of a process of interest; be they block maxima over long blocks or excesses over a high threshold.

http://www.assessment.ucar.edu/toolkit/
r-fail 1.3 File abstraction interface layer (FAIL)

This package provides a more comfortable interface to work with R data or source files in a key-value fashion.

https://github.com/mllg/fail
r-fastcluster 1.1.24 Fast hierarchical clustering routines

This package implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the SciPy package scipy.cluster.hierarchy, hclust() in R's stats package, and the flashClust package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide.

http://danifold.net/fastcluster.html
r-fastica 1.2-1 FastICA algorithms to perform ICA and projection pursuit

This package provides an implementation of the FastICA algorithm to perform independent component analysis (ICA) and projection pursuit.

http://cran.r-project.org/web/packages/fastICA
r-fastmatch 1.1-0 Fast match function

This package provides a fast match replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.

http://www.rforge.net/fastmatch
r-fastseg 1.22.0 Fast segmentation algorithm for genetic sequencing data

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

http://www.bioinf.jku.at/software/fastseg/index.html
r-fdrtool 1.2.15 Estimation of false discovery rates and higher criticism

This package provides tools to estimate both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.

http://strimmerlab.org/software/fdrtool/
r-ff 2.2-13 Memory-efficient storage of large data on disk and access functions

This package provides data structures that are stored on disk but behave (almost) as if they were in RAM by transparently mapping only a section in main memory.

http://ff.r-forge.r-project.org/
r-ffbase 0.12.3 Basic statistical functions for package 'ff'

This package extends the out of memory vectors of ff with statistical functions and other utilities to ease their usage.

http://github.com/edwindj/ffbase
r-fit-models 0.5-14 Compare fitted models

The fit.models function and its associated methods (coefficients, print, summary, plot, etc.) were originally provided in the robust package to compare robustly and classically fitted model objects. The aim of the fit.models package is to separate this fitted model object comparison functionality from the robust package and to extend it to support fitting methods (e.g., classical, robust, Bayesian, regularized, etc.) more generally.

http://cran.r-project.org/web/packages/fit.models
r-fitdistrplus 1.0-9 Fitting a parametric distribution from data

This package extends the fitdistr function of the MASS package with several functions to help the fit of a parametric distribution to non-censored or censored data. Censored data may contain left-censored, right-censored and interval-censored values, with several lower and upper bounds. In addition to maximum likelihood estimation (MLE), the package provides moment matching (MME), quantile matching (QME) and maximum goodness-of-fit estimation (MGE) methods (available only for non-censored data). Weighted versions of MLE, MME and QME are available.

http://riskassessment.r-forge.r-project.org
r-fivethirtyeight 0.1.0 Data and code behind the stories at FiveThirtyEight

This R package provides access to the code and data sets published by the statistics blog FiveThirtyEight.

https://mran.microsoft.com/package/fivethirtyeight/
r-flexmix 2.3-14 Flexible mixture modeling

This package implements a general framework for finite mixtures of regression models using the EM algorithm. FlexMix provides the E-step and all data handling, while the M-step can be supplied by the user to easily define new models. Existing drivers implement mixtures of standard linear models, generalized linear models and model-based clustering.

http://cran.r-project.org/web/packages/flexmix
r-fnn 1.1 Fast nearest neighbor search algorithms and applications

This package provides cover-tree and kd-tree fast k-nearest neighbor search algorithms and related applications including KNN classification, regression and information measures.

http://cran.r-project.org/web/packages/FNN
r-foreach 1.4.3 Foreach looping construct for R

This package provides support for the foreach looping construct. foreach is an idiom that allows for iterating over elements in a collection, without the use of an explicit loop counter. This package in particular is intended to be used for its return value, rather than for its side effects. In that sense, it is similar to the standard lapply function, but doesn't require the evaluation of a function. Using foreach without side effects also facilitates executing the loop in parallel.

http://cran.r-project.org/web/packages/foreach
r-foreign 0.8-69 Read data stored by other statistics software

This package provides functions for reading and writing data stored by some versions of Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka and for reading and writing some dBase files.

http://cran.r-project.org/web/packages/foreign
r-formatr 1.5 Format R code automatically

This package provides a function to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package.

http://yihui.name/formatR
r-formula 1.2-2 Extended model formulas

This package provides a new class Formula, which extends the base class formula. It supports extended formulas with multiple parts of regressors on the right-hand side and/or multiple responses on the left-hand side.

http://cran.r-project.org/web/packages/Formula
r-fpc 2.1-10 Flexible procedures for clustering

This package provides various methods for clustering and cluster validation. For example, it provides fixed point clustering, linear regression clustering, clustering by merging Gaussian mixture components, as well as symmetric and asymmetric discriminant projections for visualisation of the separation of groupings.

http://cran.r-project.org/web/packages/fpc
r-futile-logger 1.4.3 Logging utility for R

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

http://cran.r-project.org/web/packages/futile.logger
r-futile-options 1.0.0 Options management framework

The futile.options subsystem provides an easy user-defined options management system that is properly scoped. This means that options created via futile.options are fully self-contained and will not collide with options defined in other packages.

http://cran.r-project.org/web/packages/futile.options
r-gdata 2.18.0 Various R programming tools for data manipulation

This package provides various R programming tools for data manipulation, including:

  • medical unit conversions

  • combining objects

  • character vector operations

  • factor manipulation

  • obtaining information about R objects

  • manipulating MS-Excel formatted files

  • generating fixed-width format files

  • extricating components of date and time objects

  • operations on columns of data frames

  • matrix operations

  • operations on vectors and data frames

  • value of last evaluated expression

  • wrapper for sample that ensures consistent behavior for both scalar and vector arguments

http://cran.r-project.org/web/packages/gdata
r-gdtools 0.1.6 Utilities for graphical rendering

The gdtools package provides functionalities to get font metrics and to generate base64 encoded string from raster matrix.

http://cran.r-project.org/web/packages/gdtools
r-genefilter 1.58.0 Filter genes from high-throughput experiments

This package provides basic functions for filtering genes from high-throughput sequencing experiments.

http://bioconductor.org/packages/genefilter
r-geneplotter 1.54.0 Graphics functions for genomic data
r-genomation 1.8.0 Summary, annotation and visualization of genomic data

This package provides a package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, it can use BAM or BigWig files as input.

http://bioinformatics.mdc-berlin.de/genomation/
r-genomationdata 1.6.0 Experimental data for use with the genomation package

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

http://bioinformatics.mdc-berlin.de/genomation/
r-genomeinfodb 1.12.2 Utilities for manipulating chromosome identifiers

This package contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.

http://bioconductor.org/packages/GenomeInfoDb
r-genomeinfodbdata 0.99.0 Species and taxonomy ID look up tables for GenomeInfoDb

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.

http://bioconductor.org/packages/GenomeInfoDbData
r-genomicalignments 1.12.2 Representation and manipulation of short genomic alignments

This package provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.

http://bioconductor.org/packages/GenomicAlignments
r-genomicfeatures 1.28.4 Tools for working with transcript centric annotations

This package provides a set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.

http://bioconductor.org/packages/GenomicFeatures
r-genomicranges 1.28.4 Representation and manipulation of genomic intervals

This package provides tools to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.

http://bioconductor.org/packages/GenomicRanges
r-getopt 1.20.0 Command-line option processor for R

This package is designed to be used with Rscript to write shebang scripts that accept short and long options. Many users will prefer to use the packages optparse or argparse which add extra features like automatically generated help options and usage texts, support for default values, positional argument support, etc.

https://github.com/trevorld/getopt
r-getoptlong 0.1.6 Parsing command-line arguments and variable interpolation

This is yet another command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptation for easier use in R. It also provides a simple way for variable interpolation in R.

https://github.com/jokergoo/GetoptLong
r-ggally 1.3.2 Extension to ggplot2

The R package ggplot2 is a plotting system based on the grammar of graphics. GGally extends ggplot2 by adding several functions to reduce the complexity of combining geometric objects with transformed data. Some of these functions include a pairwise plot matrix, a two group pairwise plot matrix, a parallel coordinates plot, a survival plot, and several functions to plot networks.

https://ggobi.github.io/ggally
r-ggbeeswarm 0.6.0 Categorical scatter (violin point) plots

This package provides two methods of plotting categorical scatter plots such that the arrangement of points within a category reflects the density of data at that region, and avoids over-plotting.

https://github.com/eclarke/ggbeeswarm
r-ggdendro 0.1-20 Create Dendrograms and Tree Diagrams Using ggplot2

This is a set of tools for dendrograms and tree plots using ggplot2. The ggplot2 philosophy is to clearly separate data from the presentation. Unfortunately the plot method for dendrograms plots directly to a plot device with out exposing the data. The ggdendro package resolves this by making available functions that extract the dendrogram plot data. The package provides implementations for tree, rpart, as well as diana and agnes cluster diagrams.

https://github.com/andrie/ggdendro
r-ggplot2 2.2.1 An implementation of the grammar of graphics

Ggplot2 is an implementation of the grammar of graphics in R. It combines the advantages of both base and lattice graphics: conditioning and shared axes are handled automatically, and you can still build up a plot step by step from multiple data sources. It also implements a sophisticated multidimensional conditioning system and a consistent interface to map data to aesthetic attributes.

http://ggplot2.org
r-ggthemes 3.4.0 Extra themes, scales and geoms for ggplot2

This package provides extra themes and scales for ggplot2 that replicate the look of plots by Edward Tufte and Stephen Few in Fivethirtyeight, The Economist, Stata, Excel, and The Wall Street Journal, among others. This package also provides geoms for Tufte's box plot and range frame.

https://cran.rstudio.com/web/packages/ggthemes
r-git2r 0.19.0 Access Git repositories with R

This package provides an R interface to the libgit2 library, which is a pure C implementation of the Git core methods.

https://github.com/ropensci/git2r
r-gkmsvm 0.71.0 Gapped-kmer support vector machine

This R package provides tools for training gapped-kmer SVM classifiers for DNA and protein sequences. This package supports several sequence kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.

http://cran.r-project.org/web/packages/gkmSVM
r-glmnet 2.0-13 Lasso and elastic-net regularized generalized linear models

The glmnet package provides efficient procedures for fitting the entire lasso or elastic-net regularization path for linear and Poisson regression, as well as logistic, multinomial, Cox, multiple-response Gaussian and grouped multinomial models. The algorithm uses cyclical coordinate descent in a path-wise fashion.

http://www.jstatsoft.org/v33/i01
r-globaloptions 0.0.12 Generate functions to get or set global options

This package provides more controls on the option values such as validation and filtering on the values, making options invisible or private.

https://github.com/jokergoo/GlobalOptions
r-glue 1.1.1 Interpreted string literals

This package provides an implementation of interpreted string literals, inspired by Python's Literal String Interpolation (PEP-0498) and Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.

https://github.com/tidyverse/glue
r-go-db 3.4.0 Annotation maps describing the entire Gene Ontology

The purpose of this GO.db annotation package is to provide detailed information about the latest version of the Gene Ontologies.

http://bioconductor.org/packages/GO.db
r-googlesheets 0.2.2 Manage Google spreadsheets from R

This package provides tools to interact with Google Sheets from within R.

https://github.com/jennybc/googlesheets
r-gostats 2.42.0 Tools for manipulating GO and microarrays

This package provides a set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

http://bioconductor.org/packages/GOstats
r-gower 0.1.2 Gower's distance

This package provides tools to compute Gower's distance (or similarity) coefficient between records, and to compute the top-n matches between records. Core algorithms are executed in parallel on systems supporting OpenMP.

https://github.com/markvanderloo/gower
r-gplots 3.0.1 Various R programming tools for plotting data

This package provides various R programming tools for plotting data, including:

  • calculating and plotting locally smoothed summary function

  • enhanced versions of standard plots

  • manipulating colors

  • calculating and plotting two-dimensional data summaries

  • enhanced regression diagnostic plots

  • formula-enabled interface to stats::lowess function

  • displaying textual data in plots

  • baloon plots

  • plotting "Venn" diagrams

  • displaying Open-Office style plots

  • plotting multiple data on same region, with separate axes

  • plotting means and confidence intervals

  • spacing points in an x-y plot so they don't overlap

http://cran.r-project.org/web/packages/gplots
r-graph 1.54.0 Handle graph data structures in R

This package implements some simple graph handling capabilities for R.

http://bioconductor.org/packages/graph
r-gridbase 0.4-7 Integration of base and grid graphics

This package provides an integration of base and grid graphics for R.

http://cran.r-project.org/web/packages/gridBase
r-gridextra 2.3 Miscellaneous functions for "Grid" graphics

This package provides a number of user-level functions to work with grid graphics, notably to arrange multiple grid-based plots on a page, and draw tables.

https://github.com/baptiste/gridextra
r-grohmm 1.10.0 GRO-seq analysis pipeline

This package provides a pipeline for the analysis of GRO-seq data.

https://github.com/Kraus-Lab/groHMM
r-gseabase 1.38.0 Gene set enrichment data structures and methods

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

http://bioconductor.org/packages/GSEABase
r-gtable 0.2.0 R library to arrange grobs in tables

Gtable is a collection of tools to make it easier to work with "tables" of grobs.

https://cran.r-project.org/web/packages/gtable
r-gtools 3.5.0 Various R programming tools

This package contains a collection of various functions to assist in R programming, such as tools to assist in developing, updating, and maintaining R and R packages, calculating the logit and inverse logit transformations, tests for whether a value is missing, empty or contains only NA and NULL values, and many more.

http://cran.r-project.org/web/packages/gtools
r-hexbin 1.27.1-1 Hexagonal binning routines

This package provides binning and plotting functions for hexagonal bins. It uses and relies on grid graphics and formal (S4) classes and methods.

https://github.com/edzer/hexbin
r-highr 0.6 Syntax highlighting for R source code

This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

https://github.com/yihui/highr
r-hmisc 4.0-3 Miscellaneous data analysis and graphics functions

This package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.

http://biostat.mc.vanderbilt.edu/Hmisc
r-hms 0.3 Pretty time of day

This package implements an S3 class for storing and formatting time-of-day values, based on the difftime class.

https://github.com/rstats-db/hms
r-htmltable 1.9 Advanced tables for Markdown/HTML

This package provides functions to build tables with advanced layout elements such as row spanners, column spanners, table spanners, zebra striping, and more. While allowing advanced layout, the underlying CSS-structure is simple in order to maximize compatibility with word processors such as LibreOffice. The package also contains a few text formatting functions that help outputting text compatible with HTML or LaTeX.

http://gforge.se/packages/
r-htmltools 0.3.6 R tools for HTML

This package provides tools for HTML generation and output in R.

http://cran.r-project.org/web/packages/htmltools
r-htmlwidgets 0.9 HTML Widgets for R

HTML widgets is a framework for creating HTML widgets that render in various contexts including the R console, R Markdown documents, and Shiny web applications.

https://github.com/ramnathv/htmlwidgets
r-httpuv 1.3.5 HTTP and WebSocket server library for R

The httpuv package provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone.

https://github.com/rstudio/httpuv
r-httr 1.3.1 Tools for working with URLs and HTTP

The aim of httr is to provide a wrapper for RCurl customised to the demands of modern web APIs. It provides useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components.

https://github.com/hadley/httr
r-hwriter 1.3.2 Output R objects in HTML format

This package provides easy-to-use and versatile functions to output R objects in HTML format.

http://cran.r-project.org/web/packages/hwriter
r-igraph 1.1.2 Network analysis and visualization

This package provides routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

http://igraph.org
r-impute 1.50.0 Imputation for microarray data

This package provides a function to impute missing gene expression microarray data, using nearest neighbor averaging.

http://bioconductor.org/packages/impute
r-inline 0.3.14 Functions to inline C, C++, Fortran function calls from R

This package provides functionality to dynamically define R functions and S4 methods with inlined C, C++ or Fortran code supporting .C and .Call calling conventions.

http://cran.r-project.org/web/packages/inline
r-interactivedisplaybase 1.14.0 Base package for web displays of Bioconductor objects

This package contains the basic methods needed to generate interactive Shiny-based display methods for Bioconductor objects.

http://bioconductor.org/packages/interactiveDisplayBase
r-ipred 0.9-6 Improved predictors

This package provides improved predictive models by indirect classification and bagging for classification, regression and survival problems as well as resampling based estimators of prediction error.

http://cran.r-project.org/web/packages/ipred
r-iranges 2.10.2 Infrastructure for manipulating intervals on sequences

This package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

http://bioconductor.org/packages/IRanges
r-irlba 2.2.1 Methods for eigendecomposition of large matrices

This package provides fast and memory efficient methods for truncated singular and eigenvalue decompositions, as well as for principal component analysis of large sparse or dense matrices.

http://cran.r-project.org/web/packages/irlba
r-iterators 1.0.8 Iterator construct for R

This package provides support for iterators, which allow a programmer to traverse through all the elements of a vector, list, or other collection of data.

http://cran.r-project.org/web/packages/iterators
r-jsonlite 1.5 Robust, high performance JSON parser and generator for R

The jsonlite package provides a fast JSON parser and generator optimized for statistical data and the web. It offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with a web API. In addition to converting JSON data from/to R objects, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.

http://arxiv.org/abs/1403.2805
r-kernlab 0.9-25 Kernel-based machine learning tools

This package provides kernel-based machine learning methods for classification, regression, clustering, novelty detection, quantile regression and dimensionality reduction. Among other methods kernlab includes Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes and a QP solver.

http://cran.r-project.org/web/packages/kernlab
r-kernsmooth 2.23-15 Functions for kernel smoothing

This package provides functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".

non-copyleft (This is a lax, non-copyleft free software license. Check the URI for details. )
http://cran.r-project.org/web/packages/KernSmooth
r-knitr 1.17 General-purpose package for dynamic report generation in R

This package provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

http://yihui.name/knitr/
r-knitrbootstrap 1.0.1 Knitr bootstrap framework

This package provides a framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.

https://github.com/jimhester/knitrBootstrap
r-ksamples 1.2-7 K-Sample rank tests and their combinations

This package provides tools to compares k samples using the Anderson-Darling test, Kruskal-Wallis type tests with different rank score criteria, Steel's multiple comparison test, and the Jonckheere-Terpstra (JT) test. It computes asymptotic, simulated or (limited) exact P-values, all valid under randomization, with or without ties, or conditionally under random sampling from populations, given the observed tie pattern. Except for Steel's test and the JT test it also combines these tests across several blocks of samples.

http://cran.r-project.org/web/packages/kSamples
r-labeling 0.3 Axis labeling algorithms

The labeling package provides a range of axis labeling algorithms.

http://cran.r-project.org/web/packages/labeling
r-lambda-r 1.2 Functional programming extension for R

This package provides a language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.

http://cran.r-project.org/web/packages/lambda.r
r-lars 1.2 Least angle regression software

Least Angle Regression ("LAR") is a model selection algorithm; a useful and less greedy version of traditional forward selection methods. A simple modification of the LAR algorithm implements Tibshirani's Lasso; the Lasso modification of LARS calculates the entire Lasso path of coefficients for a given problem at the cost of a single least squares fit. Another LARS modification efficiently implements epsilon Forward Stagewise linear regression.

http://www-stat.stanford.edu/~hastie/Papers/#LARS
r-lattice 0.20-35 High-level data visualization system

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.

http://lattice.r-forge.r-project.org/
r-latticeextra 0.6-28 Extra graphical utilities based on lattice

Building on the infrastructure provided by the lattice package, this package provides several new high-level graphics functions and methods, as well as additional utilities such as panel and axis annotation functions.

http://latticeextra.r-forge.r-project.org/
r-lava 1.5.1 Latent variable models

This package provides tools for the estimation and simulation of latent variable models.

https://github.com/kkholst/lava
r-lazyeval 0.2.0 Lazy (non-standard) evaluation in R

This package provides the tools necessary to do non-standard evaluation (NSE) in R.

https://github.com/hadley/lazyeval
r-limma 3.32.5 Package for linear models for microarray and RNA-seq data

This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.

http://bioinf.wehi.edu.au/limma
r-limsolve 1.5.5.3 Solving linear inverse models

This package provides functions that:

  1. find the minimum/maximum of a linear or quadratic function,

  2. sample an underdetermined or overdetermined system,

  3. solve a linear system Ax=B for the unknown x.

It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.

http://cran.r-project.org/web/packages/limSolve
r-lme4 1.1-14 Linear mixed-effects models using eigen and S4

This package provides fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the Eigen C++ library for numerical linear algebra and RcppEigen glue.

http://cran.r-project.org/web/packages/lme4
r-lmoments 1.2-3 L-moments and quantile mixtures

This package contains functions to estimate L-moments and trimmed L-moments from the data. It also contains functions to estimate the parameters of the normal polynomial quantile mixture and the Cauchy polynomial quantile mixture from L-moments and trimmed L-moments.

http://www.tilastotiede.fi/juha_karvanen.html
r-lmtest 0.9-35 Testing linear regression models

This package provides a collection of tests, data sets, and examples for diagnostic checking in linear regression models. Furthermore, some generic tools for inference in parametric models are provided.

http://cran.r-project.org/web/packages/lmtest
r-locfit 1.5-9.1 Local regression, likelihood and density estimation

This package provides functions used for local regression, likelihood and density estimation.

http://cran.r-project.org/web/packages/locfit
r-lpsolve 5.6.13 R interface to Lp_solve to solve linear/integer programs

Lp_solve is software for solving linear, integer and mixed integer programs. This implementation supplies a "wrapper" function in C and some R functions that solve general linear/integer problems, assignment problems, and transportation problems.

http://cran.r-project.org/web/packages/lpSolve
r-lubridate 1.6.0 Make dealing with dates a little easier

This package provides functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

http://cran.r-project.org/web/packages/lubridate
r-magrittr 1.5 A forward-pipe operator for R

Magrittr provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."

http://cran.r-project.org/web/packages/magrittr/index.html
r-maldiquant 1.16.4 Quantitative analysis of mass spectrometry data

This package provides a complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.

http://cran.r-project.org/web/packages/MALDIquant
r-markdown 0.8 Markdown rendering for R

This package provides R bindings to the Sundown Markdown rendering library (https://github.com/vmg/sundown). Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.

https://github.com/rstudio/markdown
r-mass 7.3-47 Support functions and datasets for Venables and Ripley's MASS

This package provides functions and datasets for the book "Modern Applied Statistics with S" (4th edition, 2002) by Venables and Ripley.

http://www.stats.ox.ac.uk/pub/MASS4/
r-matrix 1.2-11 Sparse and dense matrix classes and methods

This package provides classes and methods for dense and sparse matrices and operations on them using LAPACK and SuiteSparse.

http://Matrix.R-forge.R-project.org/
r-matrixmodels 0.4-1 Modelling with sparse and dense matrices

This package models with sparse and dense matrix matrices, using modular prediction and response module classes.

https://cran.r-project.org/web/packages/MatrixModels
r-matrixstats 0.52.2 Methods applying to vectors and matrix rows and columns

This package provides methods operating on rows and columns of matrices, e.g. rowMedians(), rowRanks(), and rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.

https://github.com/HenrikBengtsson/matrixStats
r-mclust 5.3 Gaussian mixture modelling for model-based clustering etc.

This package provides Gaussian finite mixture models fitted via EM algorithm for model-based clustering, classification, and density estimation, including Bayesian regularization, dimension reduction for visualisation, and resampling-based inference.

http://www.stat.washington.edu/mclust/
r-memoise 1.1.0 Memoise functions for R

This R package allows to cache the results of a function so that when you call it again with the same arguments it returns the pre-computed value.

https://github.com/hadley/memoise
r-methylkit 1.2.0 DNA methylation analysis from high-throughput bisulfite sequencing results

MethylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from Reduced representation bisulfite sequencing (RRBS) and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.

http://code.google.com/p/methylkit/
r-mgcv 1.8-22 Mixed generalised additive model computation

GAMs, GAMMs and other generalized ridge regression with multiple smoothing parameter estimation by GCV, REML or UBRE/AIC. The library includes a gam() function, a wide variety of smoothers, JAGS support and distributions beyond the exponential family.

http://cran.r-project.org/web/packages/mgcv
r-microbenchmark 1.4-2.1 Accurate timing functions for R

This package provides infrastructure to accurately measure and compare the execution time of R expressions.

https://cran.r-project.org/web/packages/microbenchmark/
r-mime 0.5 R package to map filenames to MIME types

This package guesses the MIME type from a filename extension using the data derived from /etc/mime.types in UNIX-type systems.

https://github.com/yihui/mime
r-minimal 3.4.2 Environment for statistical computing and graphics

R is a language and environment for statistical computing and graphics. It provides a variety of statistical techniques, such as linear and nonlinear modeling, classical statistical tests, time-series analysis, classification and clustering. It also provides robust support for producing publication-quality data plots. A large amount of 3rd-party packages are available, greatly increasing its breadth and scope.

http://www.r-project.org/
r-minqa 1.2.4 Derivative-free optimization algorithms by quadratic approximation

This package provides a derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell.

http://optimizer.r-forge.r-project.org
r-mixtools 1.1.0 Tools for analyzing finite mixture models

This package provides a collection of R functions for analyzing finite mixture models.

http://cran.r-project.org/web/packages/mixtools
r-mnormt 1.5-5 Multivariate normal and "t" distributions

This package provides functions for computing the density and the distribution function of multivariate normal and "t" random variables, and for generating random vectors sampled from these distributions. Probabilities are computed via non-Monte Carlo methods.

http://azzalini.stat.unipd.it/SW/Pkg-mnormt
r-modelmetrics 1.1.0 Rapid calculation of model metrics

Written in C++ using Rcpp, this package provides a collection of metrics for evaluating models.

http://cran.r-project.org/web/packages/ModelMetrics
r-modeltools 0.2-21 Tools and classes for statistical models

This package provides a collection of tools to deal with statistical models. The functionality is experimental and the user interface is likely to change in the future.

http://cran.r-project.org/web/packages/modeltools
r-motifrg 1.20.0 Discover motifs in high throughput sequencing data

This package provides tools for discriminative motif discovery in high throughput genetic sequencing data sets using regression methods.

http://bioconductor.org/packages/motifRG
r-msnbase 2.2.0 Base functions and classes for MS-based proteomics

This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.

https://github.com/lgatto/MSnbase
r-msnid 1.10.0 Utilities for LC-MSn proteomics identifications

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

http://bioconductor.org/packages/MSnID
r-multitaper 1.0-13 Multitaper spectral analysis tools

This package implements multitaper spectral estimation techniques using prolate spheroidal sequences (Slepians) and sine tapers for time series analysis. It includes an adaptive weighted multitaper spectral estimate, a coherence estimate, Thomson's Harmonic F-test, and complex demodulation. The Slepians sequences are generated efficiently using a tridiagonal matrix solution, and jackknifed confidence intervals are available for most estimates.

https://github.com/wesleyburr/multitaper/
r-munsell 0.4.3 Munsell colour system

The Munsell package contains Functions for exploring and using the Munsell colour system.

http://cran.r-project.org/web/packages/munsell
r-mutationalpatterns 1.2.1 Extract and visualize mutational patterns in genomic data

This package provides an extensive toolset for the characterization and visualization of a wide range of mutational patterns in SNV base substitution data.

http://bioconductor.org/packages/MutationalPatterns/
r-mvtnorm 1.0-6 Package for multivariate normal and t-distributions

This package can compute multivariate normal and t-probabilities, quantiles, random deviates and densities.

http://mvtnorm.R-forge.R-project.org
r-mzid 1.14.0 Parser for mzIdentML files

This package provides a parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less pretty output than a vendor specific parser.

http://bioconductor.org/packages/mzID
r-mzr 2.10.0 Parser for mass spectrometry data files

The mzR package provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.

https://github.com/sneumann/mzR/
r-nlme 3.1-131 Linear and nonlinear mixed effects models

This package provides tools to fit and compare Gaussian linear and nonlinear mixed-effects models.

http://cran.r-project.org/web/packages/nlme
r-nloptr 1.0.4 R interface to NLopt

This package is interface to NLopt, a library for nonlinear optimization. NLopt is a library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.

http://cran.r-project.org/web/packages/nloptr
r-nmf 0.20.6 Algorithms and framework for nonnegative matrix factorization

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

http://renozao.github.io/NMF
r-nnet 7.3-12 Feed-forward neural networks and multinomial log-linear models

This package provides functions for feed-forward neural networks with a single hidden layer, and for multinomial log-linear models.

http://www.stats.ox.ac.uk/pub/MASS4/
r-numderiv 2016.8-1 Accurate numerical derivatives

This package provides methods for calculating accurate numerical first and second order derivatives.

https://cran.r-project.org/web/packages/numDeriv
r-openssl 0.9.7 Toolkit for encryption, signatures and certificates

This package provides R bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers. It supports RSA, DSA and NIST curves P-256, P-384 and P-521. Cryptographic signatures can either be created and verified manually or via x509 certificates. AES block cipher is used in CBC mode for symmetric encryption; RSA for asymmetric (public key) encryption. High-level envelope functions combine RSA and AES for encrypting arbitrary sized data. Other utilities include key generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random number generator, and bignum math methods for manually performing crypto calculations on large multibyte integers.

https://github.com/jeroenooms/openssl
r-optparse 1.4.4 Command line option parser

This package provides a command line parser inspired by Python's optparse library to be used with Rscript to write shebang scripts that accept short and long options.

https://github.com/trevorld/optparse
r-org-ce-eg-db 3.4.0 Genome wide annotation for Worm

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

http://www.bioconductor.org/packages/org.Ce.eg.db/
r-org-dm-eg-db 3.4.0 Genome wide annotation for Fly

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

http://www.bioconductor.org/packages/org.Dm.eg.db/
r-org-hs-eg-db 3.4.0 Genome wide annotation for Human

This package provides mappings from Entrez gene identifiers to various annotations for the human genome.

http://www.bioconductor.org/packages/org.Hs.eg.db/
r-org-mm-eg-db 3.4.0 Genome wide annotation for Mouse

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model mouse Mus musculus.

http://www.bioconductor.org/packages/org.Mm.eg.db/
r-pbapply 1.3-3 Adding progress bar to apply functions

This lightweight package that adds progress bar to vectorized R functions apply. The implementation can easily be added to functions where showing the progress is useful e.g. bootstrap.

https://github.com/psolymos/pbapply
r-pbkrtest 0.4-7 Methods for linear mixed model comparison

This package implements a parametric bootstrap test and a Kenward Roger modification of F-tests for linear mixed effects models and a parametric bootstrap test for generalized linear mixed models.

http://people.math.aau.dk/~sorenh/software/pbkrtest/
r-pcamethods 1.68.0 Collection of PCA methods

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.

https://github.com/hredestig/pcamethods
r-pcapp 1.9-72 Robust PCA by projection pursuit

This package provides functions for robust principal component analysis (PCA) by projection pursuit.

http://cran.r-project.org/web/packages/pcaPP
r-permute 0.9-4 Functions for Generating Restricted Permutations of Data

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). permute also allows split-plot designs, in which the whole-plots or split-plots or both can be freely exchangeable.

https://github.com/gavinsimpson/permute
r-pheatmap 1.0.8 Pretty heatmaps

This package provides an implementation of heatmaps that offers more control over dimensions and appearance.

http://cran.r-project.org/web/packages/pheatmap
r-pkgconfig 2.0.1 Private configuration for R packages

This package provides the functionality to set configuration options on a per-package basis. Options set by a given package only apply to that package, other packages are unaffected.

https://github.com/gaborcsardi/pkgconfig
r-pkgmaker 0.22 Package development utilities

This package provides some low-level utilities to use for R package development. It currently provides managers for multiple package specific options and registries, vignette, unit test and bibtex related utilities.

https://renozao.github.io/pkgmaker
r-plogr 0.1-1 R bindings for the plog C++ logging library

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.

https://github.com/krlmlr/plogr
r-plotly 4.7.1 Create interactive web graphics

This package enables the translation of ggplot2 graphs to an interactive web-based version and/or the creation of custom web-based visualizations directly from R. Once uploaded to a plotly account, plotly graphs (and the data behind them) can be viewed and modified in a web browser.

https://plot.ly/r
r-plotrix 3.6-6 Various plotting functions

This package provides lots of plotting, various labeling, axis and color scaling functions for R.

http://cran.r-project.org/web/packages/plotrix
r-plyr 1.8.4 Tools for Splitting, Applying and Combining Data

Plyr is a set of tools that solves a common set of problems: you need to break a big problem down into manageable pieces, operate on each piece and then put all the pieces back together. For example, you might want to fit a model to each spatial location or time point in your study, summarise data by panels or collapse high-dimensional arrays to simpler summary statistics.

http://had.co.nz/plyr
r-png 0.1-7 Read and write PNG images

This package provides an easy and simple way to read, write and display bitmap images stored in the PNG format. It can read and write both files and in-memory raw vectors.

http://www.rforge.net/png/
r-powerlaw 0.70.1 Tools for the analysis of heavy tailed distributions

This package provides an implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.

https://github.com/csgillespie/poweRlaw
r-prabclus 2.2-6 Parametric bootstrap tests for spatial neighborhood clustering

This package provides a distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection.

https://cran.r-project.org/web/packages/prabclus
r-pracma 2.0.7 Practical numerical math functions

This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some special functions. It uses Matlab function names where appropriate to simplify porting.

http://cran.r-project.org/web/packages/pracma
r-praise 1.0.0 Functions to praise users

This package provides template functions to assist in building friendly R packages that praise their users.

https://github.com/gaborcsardi/praise
r-preprocesscore 1.38.1 Collection of pre-processing functions

This package provides a library of core pre-processing and normalization routines.

https://github.com/bmbolstad/preprocessCore
r-prettyunits 1.0.2 Pretty, human readable formatting of quantities

This package provides tools for pretty, human readable formatting of quantities.

https://github.com/gaborcsardi/prettyunits
r-prodlim 1.6.1 Product-limit estimation for censored event history analysis

This package provides a fast and user-friendly implementation of nonparametric estimators for censored event history (survival) analysis with the Kaplan-Meier and Aalen-Johansen methods.

http://cran.r-project.org/web/packages/prodlim
r-progress 1.1.2 Terminal progress bars

This package provides configurable progress bars. They may include percentage, elapsed time, and/or the estimated completion time. They work in terminals, in Emacs ESS, RStudio, Windows Rgui, and the macOS R.app. The package also provides a C++ API, that works with or without Rcpp.

https://github.com/gaborcsardi/progress
r-protgenerics 1.8.0 S4 generic functions for proteomics infrastructure

This package provides S4 generic functions needed by Bioconductor proteomics packages.

https://github.com/lgatto/ProtGenerics
r-proto 1.0.0 Prototype object-based programming

Proto is an object oriented system using object-based, also called prototype-based, rather than class-based object oriented ideas.

https://github.com/hadley/proto
r-proxy 0.4-17 Distance and similarity measures

This package provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.

http://cran.r-project.org/web/packages/proxy
r-pryr 0.1.2 Tools for computing on the R language

This package provides useful tools to pry back the covers of R and understand the language at a deeper level.

https://github.com/hadley/pryr
r-purrr 0.2.3 Functional programming tools

This package completes R's functional programming tools with missing features present in other programming languages.

https://github.com/hadley/purrr
r-qtl 1.41-6 R package for analyzing QTL experiments in genetics

R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs).

Using a hidden Markov model, R/qtl allows to estimate genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans.

http://rqtl.org/
r-quadprog 1.5-5 Functions to solve quadratic programming problems

This package contains routines and documentation for solving quadratic programming problems.

http://cran.r-project.org/web/packages/quadprog
r-quantreg 5.33 Quantile regression

This package provides an estimation and inference methods for models of conditional quantiles: linear and nonlinear parametric and non-parametric models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.

http://www.r-project.org
r-qvalue 2.8.0 Q-value estimation for false discovery rate control

This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local false discovery rate (FDR) values. The q-value of a test measures the proportion of false positives incurred when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test's p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

http://github.com/jdstorey/qvalue
r-r-cache 0.12.0 Light-weight caching of objects and results

This package provides methods for caching or memoization of objects and results. With this package, any R object can be cached in a key-value storage where the key can be an arbitrary set of R objects. The cache memory is persistent (on the file system).

https://github.com/HenrikBengtsson/R.cache
r-r-methodss3 1.7.1 S3 methods simplified

This package provides methods that simplify the setup of S3 generic functions and S3 methods. Major effort has been made in making definition of methods as simple as possible with a minimum of maintenance for package developers. For example, generic functions are created automatically, if missing, and naming conflict are automatically solved, if possible. The method setMethodS3() is a good start for those who in the future may want to migrate to S4.

http://cran.r-project.org/web/packages/R.methodsS3
r-r-oo 1.21.0 R object-oriented programming with or without references

This package provides methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers.

https://github.com/HenrikBengtsson/R.oo
r-r-rsp 0.41.0 Dynamic generation of scientific reports

The RSP markup language provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. Today's date is <%=Sys.Date()%>. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. RSP is ideal for self-contained scientific reports and R package vignettes.

https://github.com/HenrikBengtsson/R.rsp
r-r-utils 2.5.0 Various programming utilities

This package provides utility functions useful when programming and developing R packages.

https://github.com/HenrikBengtsson/R.utils
r-r4rna 0.1.4 Analysis framework for RNA secondary structure

The R4RNA package aims to be a general framework for the analysis of RNA secondary structure and comparative analysis in R.

http://www.e-rna.org/r-chie/index.cgi
r-r6 2.2.2 Classes with reference semantics in R

The R6 package allows the creation of classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.

https://github.com/wch/R6/
r-randomforest 4.6-12 Breiman and Cutler's random forests for classification and regression

This package provides the Breiman and Cutler's random forests algorithm, based on a forest of trees using random inputs, for classification and regression.

https://www.stat.berkeley.edu/~breiman/RandomForests/
r-ranger 0.8.0 Fast implementation of random forests

This package provides a fast implementation of Random Forests, particularly suited for high dimensional data. Ensembles of classification, regression, survival and probability prediction trees are supported. Data from genome-wide association studies can be analyzed efficiently.

https://github.com/imbs-hl/ranger
r-rann 2.5.1 Fast nearest neighbour search

This package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library. Provides approximate, exact searches, fixed radius searches, bd and kb trees.

https://github.com/jefferis/RANN
r-raremetals2 0.1 Analyze gene-level association tests for binary trait

The R package rareMETALS2 is an extension of the R package rareMETALS. It was designed to meta-analyze gene-level association tests for binary trait. While rareMETALS offers a near-complete solution for meta-analysis of gene-level tests for quantitative trait, it does not offer the optimal solution for binary trait. The package rareMETALS2 offers improved features for analyzing gene-level association tests in meta-analyses for binary trait.

http://genome.sph.umich.edu/wiki/RareMETALS2
r-rbgl 1.52.0 Interface to the Boost graph library

This package provides a fairly extensive and comprehensive interface to the graph algorithms contained in the Boost library.

http://www.bioconductor.org/packages/RBGL
r-rcas 1.3.4 RNA-centric annotation system

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

https://github.com/BIMSBbioinfo/RCAS
r-rcolorbrewer 1.1-2 ColorBrewer palettes

This package provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org

http://cran.r-project.org/web/packages/RColorBrewer
r-rcpp 0.12.13 Seamless R and C++ integration

The Rcpp package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about Rcpp is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the paper by Eddelbuettel and Francois (2011, JSS), and the book by Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these last two.

http://www.rcpp.org
r-rcpparmadillo 0.7.960.1.2 Rcpp integration for the Armadillo linear algebra library

Armadillo is a templated C++ linear algebra library that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. This package includes the header files from the templated Armadillo library.

https://github.com/RcppCore/RcppArmadillo
r-rcppeigen 0.3.3.3.0 Rcpp integration for the Eigen templated linear algebra library

This package provides an integration of Eigen in R using a C++ template library for linear algebra: matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse matrices on integer, floating point and complex numbers, decompositions of such matrices, and solutions of linear systems.

http://eigen.tuxfamily.org
r-rcppprogress 0.3 Interruptible progress bar for C++ in R packages

This package allows to display a progress bar in the R console for long running computations taking place in C++ code, and support for interrupting those computations even in multithreaded code, typically using OpenMP.

https://github.com/kforner/rcpp_progress
r-rcpproll 0.2.2 Efficient rolling and windowed operations

This package provides fast and efficient routines for common rolling / windowed operations. Routines for the efficient computation of windowed mean, median, sum, product, minimum, maximum, standard deviation and variance are provided.

http://cran.r-project.org/web/packages/RcppRoll
r-rcurl 1.95-0.1.2 General network client interface for R

The package allows one to compose general HTTP requests and provides convenient functions to fetch URIs, GET and POST forms, etc. and process the results returned by the Web server. This provides a great deal of control over the HTTP/FTP/... connection and the form of the request while providing a higher-level interface than is available just using R socket connections. Additionally, the underlying implementation is robust and extensive, supporting FTP/FTPS/TFTP (uploads and downloads), SSL/HTTPS, telnet, dict, ldap, and also supports cookies, redirects, authentication, etc.

http://www.omegahat.org/RCurl
r-readr 1.1.1 Read tabular data

This package provides functions to read flat or tabular text files from disk (or a connection).

https://github.com/hadley/readr
r-recipes 0.1.0 Preprocessing tools to create design matrices

Recipes is an extensible framework to create and preprocess design matrices. Recipes consist of one or more data manipulation and analysis "steps". Statistical parameters for the steps can be estimated from an initial data set and then applied to other data sets. The resulting design matrices can then be used as inputs into statistical or machine learning models.

https://github.com/topepo/recipes
r-registry 0.3 Infrastructure for R package registries

This package provides a generic infrastructure for creating and using R package registries.

http://cran.r-project.org/web/packages/registry
r-rematch 1.0.1 Match regular expressions with a nicer API

This package provides a small wrapper on regexpr to extract the matches and captured groups from the match of a regular expression to a character vector.

https://github.com/MangoTheCat/rematch
r-reshape 0.8.7 Flexibly reshape data

Flexibly restructure and aggregate data using just two functions: melt and cast. This package provides them.

http://had.co.nz/reshape
r-reshape2 1.4.2 Flexibly reshape data: a reboot of the "reshape" package

Reshape2 is an R library to flexibly restructure and aggregate data using just two functions: melt and dcast (or acast).

https://github.com/hadley/reshape
r-rhdf5 2.20.0 HDF5 interface to R

This R/Bioconductor package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

http://bioconductor.org/packages/rhdf5
r-rhtslib 1.8.0 High-throughput sequencing library as an R package

This package provides the HTSlib C library for high-throughput nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.

https://github.com/nhayden/Rhtslib
r-rjson 0.2.15 JSON library for R

This package provides functions to convert R objects into JSON objects and vice-versa.

http://cran.r-project.org/web/packages/rjson
r-rlang 0.1.2 Functions for base types, core R and Tidyverse features

This package provides a toolbox for working with base types, core R features like the condition system, and core Tidyverse features like tidy evaluation.

http://rlang.tidyverse.org
r-rmarkdown 1.6 Convert R Markdown documents into a variety of formats

This package provides tools to convert R Markdown documents into a variety of formats.

http://rmarkdown.rstudio.com
r-rmtstat 0.3 Distributions, statistics and tests derived from random matrix theory

This package provides functions for working with the Tracy-Widom laws and other distributions related to the eigenvalues of large Wishart matrices.

http://cran.r-project.org/web/packages/RMTstat
r-rngtools 1.2.4 Utility functions for working with random number generators

This package contains a set of functions for working with Random Number Generators (RNGs). In particular, it defines a generic S4 framework for getting/setting the current RNG, or RNG data that are embedded into objects for reproducibility. Notably, convenient default methods greatly facilitate the way current RNG settings can be changed.

https://renozao.github.io/rngtools
r-robust 0.4-18 Port of the S+ "Robust Library"

This package is a port of the S+ "Robust Library". It provides methods for robust statistics, notably for robust regression and robust multivariate analysis.

http://cran.r-project.org/web/packages/robust
r-robustbase 0.92-7 Basic robust statistics

This packages allows to analyze data with robust methods such as regression methodology including model selections and multivariate statistics.

http://robustbase.r-forge.r-project.org/
r-rocr 1.0-7 Visualizing the performance of scoring classifiers

ROCR is a flexible tool for creating cutoff-parameterized 2D performance curves by freely combining two from over 25 performance measures (new performance measures can be added using a standard interface). Curves from different cross-validation or bootstrapping runs can be averaged by different methods, and standard deviations, standard errors or box plots can be used to visualize the variability across the runs. The parameterization can be visualized by printing cutoff values at the corresponding curve positions, or by coloring the curve according to cutoff. All components of a performance plot can be quickly adjusted using a flexible parameter dispatching mechanism.

http://rocr.bioinf.mpi-sb.mpg.de/
r-rook 1.1-1 Web server interface for R

This package contains the Rook specification and convenience software for building and running Rook applications. A Rook application is an R reference class object that implements a call method or an R closure that takes exactly one argument, an environment, and returns a list with three named elements: the status, the headers, and the body.

http://cran.r-project.org/web/packages/Rook
r-roxygen2 6.0.1 In-source documentation system for R

Roxygen2 is a Doxygen-like in-source documentation system for Rd, collation, and NAMESPACE files.

https://github.com/klutometis/roxygen
r-rpart 4.1-11 Recursive partitioning and regression trees

This package provides recursive partitioning functions for classification, regression and survival trees.

http://cran.r-project.org/web/packages/rpart
r-rprojroot 1.2 Finding files in project subdirectories

This package helps accessing files relative to a project root. It provides helpers for robust, reliable and flexible paths to files below a project root. The root of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

https://github.com/krlmlr/rprojroot
r-rrcov 1.4-3 Scalable robust estimators with high breakdown Point

This package provides an implementation of robust location and scatter estimation and robust multivariate analysis with high breakdown point.

http://cran.r-project.org/web/packages/rrcov
r-rsamtools 1.28.0 Interface to samtools, bcftools, and tabix

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

http://bioconductor.org/packages/release/bioc/html/Rsamtools.html
r-rsqlite 2.0 SQLite interface for R

This package embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine (version 3.8.8.2) is included.

https://github.com/rstats-db/RSQLite
r-rstudioapi 0.7 Safely access the RStudio API

This package provides functions to access the RStudio API and provide informative error messages when it's not available.

http://cran.r-project.org/web/packages/rstudioapi
r-rtracklayer 1.36.4 R interface to genome browsers and their annotation tracks

rtracklayer is an extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.

http://bioconductor.org/packages/rtracklayer
r-rtsne 0.13 T-distributed stochastic neighbor embedding

This package provides an R wrapper around the fast T-distributed Stochastic Neighbor Embedding using a Barnes-Hut implementation.

https://github.com/jkrijthe/Rtsne
r-runit 0.4.31 R unit test framework

This package provides R functions implementing a standard unit testing framework, with additional code inspection and report generation tools.

http://cran.r-project.org/web/packages/RUnit
r-rversions 1.0.3 Query R versions, including 'r-release' and 'r-oldrel'

This package provides functions to query the main R repository to find the versions that r-release and r-oldrel refer to, and also all previous R versions and their release dates.

https://github.com/metacran/rversions
r-s4vectors 0.14.3 S4 implementation of vectors and lists

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself.

http://bioconductor.org/packages/S4Vectors
r-scales 0.5.0 Scale functions for visualization

This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.

https://github.com/hadley/scales
r-segmented 0.5-2.2 Regression models with breakpoints estimation

Given a regression model, segmented updates the model by adding one or more segmented (i.e., piecewise-linear) relationships. Several variables with multiple breakpoints are allowed.

http://cran.r-project.org/web/packages/segmented
r-sendmailr 1.2-1 Send email using R

This package contains a simple SMTP client which provides a portable solution for sending email, including attachments, from within R.

http://cran.r-project.org/web/packages/sendmailR
r-seqgl 1.1.4 Group lasso for Dnase/ChIP-seq data

SeqGL is a group lasso based algorithm to extract transcription factor sequence signals from ChIP, DNase and ATAC-seq profiles. This package presents a method which uses group lasso to discriminate between bound and non bound genomic regions to accurately identify transcription factors bound at the specific regions.

https://github.com/ManuSetty/SeqGL
r-seqinr 3.4-5 Biological sequences retrieval and analysis

This package provides tools for exploratory data analysis and data visualization of biological sequence (DNA and protein) data. It also includes utilities for sequence data management under the ACNUC system.

http://seqinr.r-forge.r-project.org/
Sequence logos for DNA sequence alignments

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

http://bioconductor.org/packages/seqLogo
r-seqminer 6.0 Read nucleotide sequence data (VCF, BCF, and METAL formats)

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.

http://seqminer.genomic.codes
r-seqpattern 1.8.0 Visualising oligonucleotide patterns and motif occurrences

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

http://bioconductor.org/packages/seqPattern
r-servr 0.7 Simple HTTP server to serve static files or dynamic documents

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

https://github.com/yihui/servr
r-seurat 1.4.0.12-1.fccb77d Seurat is an R toolkit for single cell genomics

This package is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. It easily enables widely-used analytical techniques, including the identification of highly variable genes, dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering algorithms; density clustering, hierarchical clustering, k-means, and the discovery of differentially expressed genes and markers.

http://www.satijalab.org/seurat
patches: snippet

r-sfsmisc 1.1-1 Utilities from "Seminar fuer Statistik" ETH Zurich

This package provides useful utilities from Seminar fuer Statistik ETH Zurich, including many that are related to graphics.

http://cran.r-project.org/web/packages/sfsmisc
r-shape 1.4.3 Functions for plotting graphical shapes

This package provides functions for plotting graphical shapes such as ellipses, circles, cylinders, arrows, ...

http://cran.r-project.org/web/packages/shape
r-shiny 1.0.3 Easy interactive web applications with R

Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive prebuilt widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort.

http://shiny.rstudio.com
r-shortread 1.34.0 FASTQ input and manipulation tools

This package implements sampling, iteration, and input of FASTQ files. It includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

http://bioconductor.org/packages/ShortRead
r-sn 1.5-0 The skew-normal and skew-t distributions

This packages provides functionalities to build and manipulate probability distributions of the skew-normal family and some related ones, notably the skew-t family, and provides related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.

http://azzalini.stat.unipd.it/SN
r-snow 0.4-2 Support for simple parallel computing in R

The snow package provides support for simple parallel computing on a network of workstations using R. A master R process calls makeCluster to start a cluster of worker processes; the master process then uses functions such as clusterCall and clusterApply to execute R code on the worker processes and collect and return the results on the master.

http://cran.r-project.org/web/packages/snow
r-sourcetools 0.1.6 Tools for reading, tokenizing and parsing R code

The sourcetools package provides both an R and C++ interface for the tokenization of R code, and helpers for interacting with the tokenized representation of R code.

http://cran.r-project.org/web/packages/sourcetools
r-sp 1.2-5 Classes and methods for spatial data

This package provides classes and methods for spatial data; the classes document where the spatial location information resides, for 2D or 3D data. Utility functions are provided, e.g. for plotting data as maps, spatial selection, as well as methods for retrieving coordinates, for subsetting, print, summary, etc.

http://cran.r-project.org/web/packages/sp
r-spams 2.6-2017-03-22 Toolbox for solving sparse estimation problems

SPAMS (SPArse Modeling Software) is an optimization toolbox for solving various sparse estimation problems. It includes tools for the following problems:

  1. Dictionary learning and matrix factorization (NMF, sparse principle component analysis (PCA), ...)

  2. Solving sparse decomposition problems with LARS, coordinate descent, OMP, SOMP, proximal methods

  3. Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse group lasso, tree-structured regularization, structured sparsity with overlapping groups,...).

http://spams-devel.gforge.inria.fr
r-sparql 1.16 SPARQL client for R

This package provides an interface to use SPARQL to pose SELECT or UPDATE queries to an end-point.

http://cran.r-project.org/web/packages/SPARQL
r-sparsem 1.77 Sparse linear algebra

This package provides some basic linear algebra functionality for sparse matrices. It includes Cholesky decomposition and backsolving as well as standard R subsetting and Kronecker products.

http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html
r-spatial 7.3-11 Functions for kriging and point pattern analysis

This package provides functions for kriging and point pattern analysis.

http://www.stats.ox.ac.uk/pub/MASS4/
r-statmod 1.4.30 Statistical modeling

This package provides a collection of algorithms and functions to aid statistical modeling. It includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. It also includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.

http://cran.r-project.org/web/packages/statmod
r-stringi 1.1.5 Character string processing facilities

This package allows for fast, correct, consistent, portable, as well as convenient character string/text processing in every locale and any native encoding. Owing to the use of the ICU library, the package provides R users with platform-independent functions known to Java, Perl, Python, PHP, and Ruby programmers. Among available features there are: pattern searching (e.g. via regular expressions), random string generation, string collation, transliteration, concatenation, date-time formatting and parsing, etc.

http://stringi.rexamine.com/
r-stringr 1.2.0 Simple, consistent wrappers for common string operations

Stringr is a consistent, simple and easy to use set of wrappers around the fantastic 'stringi' package. All function and argument names (and positions) are consistent, all functions deal with "NA"'s and zero length vectors in the same way, and the output from one function is easy to feed into the input of another.

https://github.com/hadley/stringr
r-summarizedexperiment 1.6.3 Container for representing genomic ranges by sample

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

http://bioconductor.org/packages/SummarizedExperiment
r-suppdists 1.1-9.4 Supplementary distributions

This package provides ten distributions supplementing those built into R. Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi squared, Spearman's rho, maximum F ratio, the Pearson product moment correlation coefficient, Johnson distributions, normal scores and generalized hypergeometric distributions. In addition two random number generators of George Marsaglia are included.

http://cran.r-project.org/web/packages/SuppDists
r-survival 2.41-3 Survival analysis

This package contains the core survival analysis routines, including definition of Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models, and parametric accelerated failure time models.

https://github.com/therneau/survival
r-sva 3.24.4 Surrogate variable analysis

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

http://bioconductor.org/packages/sva
r-svglite 1.2.1 SVG graphics device

svglite is a graphics device that produces clean SVG (Scalable Vector Graphics) output, suitable for use on the web, or hand editing. Compared to the built-in svg(), svglite is considerably faster, produces smaller files, and leaves text as is.

https://github.com/hadley/svglite
r-synchronicity 1.1.9.1 Boost mutex functionality in R

This package provides support for synchronization via mutexes and may eventually support interprocess communication and message passing.

http://www.bigmemory.org
r-systempiper 1.10.0 Next generation sequencing workflow and reporting environment

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.

https://github.com/tgirke/systemPipeR
r-tclust 1.3-1 Robust trimmed clustering

This package implements different robust clustering algorithms (tclust) based on trimming and including some graphical diagnostic tools (ctlcurves and DiscrFact).

http://cran.r-project.org/web/packages/tclust
r-testthat 1.0.2 Unit testing for R

This package provides a unit testing system for R designed to be fun, flexible and easy to set up.

https://github.com/hadley/testthat
r-tibble 1.3.4 Simple data frames

This package provides a tbl_df class that offers better checking and printing capabilities than traditional data frames.

https://github.com/hadley/tibble
r-tidyr 0.7.1 Tidy data with `spread()` and `gather()` functions

tidyr is a reframing of the reshape2 package designed to accompany the tidy data framework, and to work hand-in-hand with magrittr and dplyr to build a solid pipeline for data analysis. It is designed specifically for tidying data, not the general reshaping that reshape2 does, or the general aggregation that reshape did. In particular, built-in methods only work for data frames, and tidyr provides no margins or aggregation.

https://github.com/hadley/tidyr
r-tidyselect 0.2.0 Select from a set of strings

This package provides a backend for the selecting functions of the tidyverse. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other tidyverse interfaces for selection.

http://cran.r-project.org/web/packages/tidyselect
r-timedate 3012.100 Chronological and calendar objects

This package provides an environment for teaching "Financial Engineering and Computational Finance" and for managing chronological and calendar objects.

https://www.rmetrics.org
r-topgo 2.28.0 Enrichment analysis for gene ontology

The topGO package provides tools for testing gene ontology (GO) terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.

http://bioconductor.org/packages/topGO
r-trimcluster 0.1-2 Cluster analysis with trimming

The trimmed k-means clustering method by Cuesta-Albertos, Gordaliza and Matran (1997). This optimizes the k-means criterion under trimming a portion of the points.

http://cran.r-project.org/web/packages/trimcluster
r-tsne 0.1-3 t-Distributed Stochastic Neighbor Embedding for R

This package provides a pure R implementation of the t-SNE algorithm.

https://github.com/jdonaldson/rtsne/
r-txdb-hsapiens-ucsc-hg19-knowngene 3.2.2 Annotation package for human genome in TxDb format

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/
r-txdb-mmusculus-ucsc-mm10-knowngene 3.4.0 Annotation package for TxDb knownGene object(s) for Mouse

This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.

http://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/
r-tximport 1.4.0 Import and summarize transcript-level estimates for gene-level analysis

This package provides tools to import transcript-level abundance, estimated counts and transcript lengths, and to summarize them into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

http://bioconductor.org/packages/tximport
r-variantannotation 1.22.3 Package for annotation of genetic variants

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.

https://bioconductor.org/packages/VariantAnnotation
r-vegan 2.4-4 Functions for community ecology

The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.

https://cran.r-project.org/web/packages/vegan
r-vgam 1.0-4 Vector generalized linear and additive models

This package is an implementation of about 6 major classes of statistical regression models. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate generalised linear models.

https://www.stat.auckland.ac.nz/~yee/VGAM
r-vipor 0.4.5 Plot categorical data using noise and density estimates

This package provides tools to generate a violin point plot, a combination of a violin/histogram plot and a scatter plot by offsetting points within a category based on their density using quasirandom noise.

http://cran.r-project.org/web/packages/vipor
r-viridis 0.4.0 Matplotlib default color map

This package is a port of the new http://matplotlib.org/ color maps (viridis--the default--, magma, plasma, and inferno) to R. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness.

https://github.com/sjmgarnier/viridis
r-viridislite 0.2.0 Default color maps from matplotlib

This package is a port of the new matplotlib color maps ('viridis', 'magma', 'plasma' and 'inferno') to R. matplotlib is a popular plotting library for Python. These color maps are designed in such a way that they will analytically be perfectly perceptually-uniform, both in regular form and also when converted to black-and-white. They are also designed to be perceived by readers with the most common form of color blindness. This is the 'lite' version of the more complete viridis package.

https://github.com/sjmgarnier/viridisLite
r-vsn 3.44.0 Variance stabilization and calibration for microarray data

The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

http://bioconductor.org/packages/release/bioc/html/vsn.html
r-wgcna 1.61 Weighted correlation network analysis

This package provides functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data. It includes functions for rudimentary data cleaning, construction and summarization of correlation networks, module identification and functions for relating both variables and modules to sample traits. It also includes a number of utility functions for data manipulation and visualization.

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/
r-whisker 0.3-2 Logicless mustache templating for R

This package provides logicless templating, with a syntax that is not limited to R.

https://github.com/edwindj/whisker
r-withr 2.0.0 Run code with temporarily modified global state

This package provides a set of functions to run R code in an environment in which global state has been temporarily modified. Many of these functions were originally a part of the r-devtools package.

https://github.com/jimhester/withr
r-xml 3.98-1.9 Tools for parsing and generating XML within R

Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an XPath "interpreter".

http://www.omegahat.org/RSXML
r-xml2 1.1.1 Parse XML with R

This package provides a simple, consistent interface to working with XML files in R. It is built on top of the libxml2 C library.

https://github.com/hadley/xml2
r-xnomial 1.0.4 Goodness-of-Fit test for multinomial data

This package provides an exact Goodness-of-Fit test for multinomial data with fixed probabilities. It can be used to determine whether a set of counts fits a given expected ratio. To see whether a set of observed counts fits an expectation, one can examine all possible outcomes with xmulti() or a random sample of them with xmonte() and find the probability of an observation deviating from the expectation by at least as much as the observed. As a measure of deviation from the expected, one can use the log-likelihood ratio, the multinomial probability, or the classic chi-square statistic. A histogram of the test statistic can also be plotted and compared with the asymptotic curve.

http://cran.r-project.org/web/packages/XNomial
r-xtable 1.8-2 Export R tables to LaTeX or HTML

This package provides tools to export R data as LaTeX and HTML tables.

http://xtable.r-forge.r-project.org/
r-xvector 0.16.0 Representation and manpulation of external sequences

This package provides memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).

http://bioconductor.org/packages/XVector
r-yaml 2.1.14 Methods to convert R data to YAML and back

This package implements the libyaml YAML 1.1 parser and emitter (http://pyyaml.org/wiki/LibYAML) for R.

https://cran.r-project.org/web/packages/yaml/
r-zlibbioc 1.22.0 Provider for zlib-1.2.5 to R packages

This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.

https://bioconductor.org/packages/zlibbioc
r-zoo 1.8-0 S3 infrastructure for regular and irregular time series

This package contains an S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors.

http://zoo.R-Forge.R-project.org/
r-ztable 0.1.5 Zebra-striped tables in LaTeX and HTML formats for R

This package provides functions to make zebra-striped tables (tables with alternating row colors) in LaTeX and HTML formats easily from data.frame, matrix, lm, aov, anova, glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.

http://cran.r-project.org/web/packages/ztable
racket 6.8 Implementation of Scheme and related languages

Racket is an implementation of the Scheme programming language (R5RS and R6RS) and related languages, such as Typed Racket. It features a compiler and a virtual machine with just-in-time native compilation, as well as a large set of libraries.

http://racket-lang.org
radare2 1.6.0 Portable reversing framework

Radare project started as a forensics tool, a scriptable commandline hexadecimal editor able to open disk files, but later support for analyzing binaries, disassembling code, debugging programs, attaching to remote gdb servers, ...

https://radare.org/
patches: snippet

radeontop 1.0 Usage monitor for AMD Radeon graphics

RadeonTop monitors resource consumption on supported AMD Radeon Graphics Processing Units (GPUs), either in real time as bar graphs on a terminal or saved to a file for further processing. It measures both the activity of the GPU as a whole, which is also accurate during OpenCL computations, as well as separate component statistics that are only meaningful under OpenGL graphics workloads.

https://github.com/clbr/radeontop/
radicale 1.1.2 Basic CalDAV and CardDAV server

Radicale is a CalDAV and CardDAV server for UNIX-like platforms. Calendars and address books are available for both local and remote access, possibly limited through authentication policies. They can be viewed and edited by calendar and contact clients on mobile phones or computers.

Radicale intentionally does not fully comply with the CalDAV and CardDAV RFCs. Instead, it supports the CalDAV and CardDAV implementations of popular clients.

http://radicale.org/
rage 0.2.1 Video and audio player based on EFL

Rage is a video and audio player written with Enlightenment Foundation Libraries with some extra bells and whistles.

https://www.enlightenment.org/about-rage
ragel 6.9 State machine compiler

Ragel compiles executable finite state machines from regular languages. Ragel targets C, C++, Obj-C, C#, D, Java, Go and Ruby. Ragel state machines can not only recognize byte sequences as regular expression machines do, but can also execute code at arbitrary points in the recognition of a regular language. Code embedding is done using inline operators that do not disrupt the regular language syntax.

http://www.colm.net/open-source/ragel/
raincat 1.1.1.3 Puzzle game with a cat in lead role

Project Raincat is a game developed by Carnegie Mellon students through GCS during the Fall 2008 semester. Raincat features game play inspired from classics Lemmings and The Incredible Machine. The project proved to be an excellent learning experience for the programmers. Everything is programmed in Haskell.

http://www.bysusanlin.com/raincat/
rakarrack 0.6.1 Audio effects processor

Rakarrack is a richly featured multi-effects processor emulating a guitar effects pedalboard. Effects include compressor, expander, noise gate, equalizers, exciter, flangers, chorus, various delay and reverb effects, distortion modules and many more. Most of the effects engine is built from modules found in the excellent software synthesizer ZynAddSubFX. Presets and user interface are optimized for guitar, but Rakarrack processes signals in stereo while it does not apply internal band-limiting filtering, and thus is well suited to all musical instruments and vocals.

http://rakarrack.sourceforge.net/
patches: snippet

randomjungle 2.1.0 Implementation of the Random Forests machine learning method

Random Jungle is an implementation of Random Forests. It is supposed to analyse high dimensional data. In genetics, it can be used for analysing big Genome Wide Association (GWA) data. Random Forests is a powerful machine learning method. Most interesting features are variable selection, missing value imputation, classifier creation, generalization error estimation and sample proximities between pairs of cases.

http://www.imbs-luebeck.de/imbs/de/node/227/
randrproto 1.5.0 Xorg RandRProto protocol headers

Resize and Rotate Extension defines a protocol for clients to dynamically change X screens, so as to resize, rotate and reflect the root window of a screen.

https://www.x.org/wiki/
rapicorn 16.0.0 Toolkit for rapid development of user interfaces

Rapicorn is a toolkit for rapid development of user interfaces in C++ and Python. The user interface is designed in a declarative markup language and is connected to the programming logic using data bindings and commands.

http://rapicorn.org
patches: 1

rapidjson 1.1.0 JSON parser/generator for C++ with both SAX/DOM style API

RapidJSON is a fast JSON parser/generator for C++ with both SAX/DOM style API.

https://github.com/miloyip/rapidjson
raptor2 2.0.15 RDF syntax library

Raptor is a C library providing a set of parsers and serialisers that generate Resource Description Framework (RDF) triples by parsing syntaxes or serialise the triples into a syntax. The supported parsing syntaxes are RDF/XML, N-Quads, N-Triples 1.0 and 1.1, TRiG, Turtle 2008 and 2013, RDFa 1.0 and 1.1, RSS tag soup including all versions of RSS, Atom 1.0 and 0.3, GRDDL and microformats for HTML, XHTML and XML. The serialising syntaxes are RDF/XML (regular, abbreviated, XMP), Turtle 2013, N-Quads, N-Triples 1.1, Atom 1.0, RSS 1.0, GraphViz DOT, HTML and JSON.

http://librdf.org/raptor/
patches: 1

rasqal 0.9.33 RDF query library

Rasqal is a C library that handles Resource Description Framework (RDF) query language syntaxes, query construction and execution of queries returning results as bindings, boolean, RDF graphs/triples or syntaxes. The supported query languages are SPARQL Query 1.0, SPARQL Query 1.1, SPARQL Update 1.1 (no executing) and the Experimental SPARQL extensions (LAQRS). Rasqal can write binding query results in the SPARQL XML, SPARQL JSON, CSV, TSV, HTML, ASCII tables, RDF/XML and Turtle/N3 and read them in SPARQL XML, RDF/XML and Turtle/N3.

http://librdf.org/rasqal/
ratpoison 1.4.9 Simple mouse-free tiling window manager

Ratpoison is a simple window manager with no fat library dependencies, no fancy graphics, no window decorations, and no rodent dependence. It is largely modelled after GNU Screen which has done wonders in the virtual terminal market.

The screen can be split into non-overlapping frames. All windows are kept maximized inside their frames to take full advantage of your precious screen real estate.

All interaction with the window manager is done through keystrokes. Ratpoison has a prefix map to minimize the key clobbering that cripples Emacs and other quality pieces of software.

http://www.nongnu.org/ratpoison/
patches: 1

raul 0.8.0 Real-time audio utility library

Raul (Real-time Audio Utility Library) is a C++ utility library primarily aimed at audio/musical applications.

http://drobilla.net/software/raul/
raul 0.8.4-1.f8bf77d3c Real-time audio utility library

Raul (Real-time Audio Utility Library) is a C++ utility library primarily aimed at audio/musical applications.

http://drobilla.net/software/raul/
raxml 8.2.10 Randomized Axelerated Maximum Likelihood phylogenetic trees

RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.

http://sco.h-its.org/exelixis/web/software/raxml/index.html
rc 1.7.4 Alternative implementation of the rc shell by Byron Rakitzis

This is a reimplementation by Byron Rakitzis of the Plan 9 shell. It has a small feature set similar to a traditional Bourne shell.

https://github.com/rakitzis/rc
rcas-web 0.0.4 Web interface for RNA-centric annotation system (RCAS)

This package provides a simple web interface for the RNA-centric annotation system (RCAS).

https://github.com/BIMSBbioinfo/rcas-web
Part of GNU rcs 5.9.4 Per-file local revision control system

RCS is the original Revision Control System. It works on a file-by-file basis, in contrast to subsequent version control systems such as CVS, Subversion, and Git. This can make it suitable for system administration files, for example, which are often inherently local to one machine.

https://www.gnu.org/software/rcs/
patches: 1

rdesktop 1.8.3 Client for Windows Terminal Services

rdesktop is a client for Microsoft's Windows Remote Desktop Services, capable of natively speaking Remote Desktop Protocol (RDP). It allows users to remotely control a user's Windows desktop.

http://www.rdesktop.org/
rdiff-backup 1.2.8 Local/remote mirroring+incremental backup

Rdiff-backup backs up one directory to another, possibly over a network. The target directory ends up a copy of the source directory, but extra reverse diffs are stored in a special subdirectory of that target directory, so you can still recover files lost some time ago. The idea is to combine the best features of a mirror and an incremental backup. Rdiff-backup also preserves subdirectories, hard links, dev files, permissions, uid/gid ownership, modification times, extended attributes, acls, and resource forks. Also, rdiff-backup can operate in a bandwidth efficient manner over a pipe, like rsync. Thus you can use rdiff-backup and ssh to securely back a hard drive up to a remote location, and only the differences will be transmitted. Finally, rdiff-backup is easy to use and settings have sensible defaults.

http://www.nongnu.org/rdiff-backup/
rdma-core 14 Utilities and libraries for working with RDMA devices

This package provides userspace components for the InfiniBand subsystem of the Linux kernel. Specifically it contains userspace libraries for the following device nodes:

  1. /dev/infiniband/uverbsX (libibverbs)

  2. /dev/infiniband/rdma_cm (librdmacm)

  3. /dev/infiniband/umadX (libibumad)

The following service daemons are also provided:

  1. srp_daemon (for the ib_srp kernel module)

  2. iwpmd (for iWARP kernel providers)

  3. ibacm (for InfiniBand communication management assistant)

X11-style (This is an X11-style, non-copyleft free software license. Check the URI for details. )
https://github.com/linux-rdma/rdma-core
rdmd 2.073.0 Specialized equivalent to 'make' for the D language

rdmd is a companion to the dmd compiler that simplifies the typical edit-compile-link-run or edit-make-run cycle to a rapid edit-run cycle. Like make and other tools, rdmd uses the relative dates of the files involved to minimize the amount of work necessary. Unlike make, rdmd tracks dependencies and freshness without requiring additional information from the user.

https://github.com/D-Programming-Language/tools/
rdup 1.1.14 Provide a list of files to backup

Rdup is a utility inspired by rsync and the plan9 way of doing backups. Rdup itself does not backup anything, it only print a list of absolute file names to standard output. Auxiliary scripts are needed that act on this list and implement the backup strategy.

http://archive.miek.nl/projects/rdup/index.html
patches: snippet

re2 2017-08-01 Fast, safe, thread-friendly regular expression engine

RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl and Python. It is a C++ library.

https://github.com/google/re2
re2c 0.16 Lexer generator for C/C++

re2c generates minimalistic hard-coded state machine (as opposed to full-featured table-based lexers). Flexible API allows generated code to be wired into virtually any environment. Instead of exposing traditional yylex() style API, re2c exposes its internals. Be sure to take a look at examples, they cover a lot of real-world cases and shed some light on dark corners of re2c API.

http://re2c.org/
Part of GNU readline 7.0 Edit command lines while typing, with history support

The GNU readline library allows users to edit command lines as they are typed in. It can maintain a searchable history of previously entered commands, letting you easily recall, edit and re-enter past commands. It features both Emacs-like and vi-like keybindings, making its usage comfortable for anyone.

https://savannah.gnu.org/projects/readline/
patches: 1

Part of GNU readline 6.2 Edit command lines while typing, with history support

The GNU readline library allows users to edit command lines as they are typed in. It can maintain a searchable history of previously entered commands, letting you easily recall, edit and re-enter past commands. It features both Emacs-like and vi-like keybindings, making its usage comfortable for anyone.

https://savannah.gnu.org/projects/readline/
patches: 1

recode 3.7.0.201402 Text encoding converter

The Recode library converts files between character sets and usages. It recognises or produces over 200 different character sets (or about 300 if combined with an iconv library) and transliterates files between almost any pair. When exact transliteration are not possible, it gets rid of offending characters or falls back on approximations. The recode program is a handy front-end to the library.

https://github.com/pinard/Recode
recordmydesktop 0.3.8.1 Desktop session video recorder

recordMyDesktop is a command-line tool that captures the activity in your graphical desktop and encodes it as a video. This is a useful tool for making screencasts.

http://recordmydesktop.sourceforge.net/
recordproto 1.14.2 Xorg RecordProto protocol headers

Record Extension defines a protocol for the recording and playback of user actions in the X Window System.

https://www.x.org/wiki/
Part of GNU recutils 1.7 Manipulate plain text files as databases

GNU Recutils is a set of tools and libraries for creating and manipulating text-based, human-editable databases. Despite being text-based, databases created with Recutils carry all of the expected features such as unique fields, primary keys, time stamps and more. Many different field types are supported, as is encryption.

https://www.gnu.org/software/recutils/
red-eclipse 1.5.8-2 Arena shooter derived from the Cube 2 engine

Red Eclipse is an arena shooter, created from the Cube2 engine. Offering an innovative parkour system and distinct but all potent weapons, Red Eclipse provides fast paced and accessible gameplay.

http://redeclipse.net/
redis 4.0.1 Key-value cache and store

Redis is an advanced key-value cache and store. Redis supports many data structures including strings, hashes, lists, sets, sorted sets, bitmaps and hyperloglogs.

http://redis.io/
redland 1.0.17 RDF library

The Redland RDF Library (librdf) provides the RDF API and triple stores.

http://librdf.org/
redshift 1.11 Adjust the color temperature of your screen

Redshift adjusts the color temperature according to the position of the sun. A different color temperature is set during night and daytime. During twilight and early morning, the color temperature transitions smoothly from night to daytime temperature to allow your eyes to slowly adapt. At night the color temperature should be set to match the lamps in your room.

https://github.com/jonls/redshift
reducelcs 1.0-1.474f88d Approximate Longest Commons Subsequence computation tool

reduceLCS is an implementation of the Reduce-Expand algorithm for LCS. It is a fast program to compute the approximate Longest Commons Subsequence of a set of strings.

https://github.com/gdv/Reduce-Expand-for-LCS
remind 3.1.15 Sophisticated calendar and alarm program

Remind allows you to remind yourself of upcoming events and appointments. Each reminder or alarm can consist of a message sent to standard output, or a program to be executed. It also features: sophisticated date calculation, moon phases, sunrise/sunset, Hebrew calendar, alarms, PostScript output and proper handling of holidays.

http://www.roaringpenguin.com/products/remind/
renderproto 0.11.1 Xorg RenderProto protocol headers

Rendering Extension defines a protcol for a digital image composition as the foundation of a new rendering model within the X Window System.

https://www.x.org/wiki/
rep-gtk 0.90.8.2 GTK+ binding for librep

Rep-GTK is a GTK+ (and GLib, GDK) binding to the librep, and one of the backend of Sawfish.

http://sawfish.wikia.com/wiki/Rep-GTK
patches: snippet

reposurgeon 3.37 Edit version-control repository history

Reposurgeon enables risky operations that version-control systems don't want to let you do, such as editing past comments and metadata and removing commits. It works with any version control system that can export and import Git fast-import streams, including Git, Mercurial, Fossil, Bazaar, CVS, RCS, and Src. It can also read Subversion dump files directly and can thus be used to script production of very high-quality conversions from Subversion to any supported Distributed Version Control System (DVCS).

http://www.catb.org/~esr/reposurgeon/
reptyr 0.6.2 Tool for reparenting a running program to a new terminal

reptyr is a utility for taking an existing running program and attaching it to a new terminal. Started a long-running process over ssh, but have to leave and don't want to interrupt it? Just start a screen, use reptyr to grab it, and then kill the ssh session and head on home.

https://github.com/nelhage/reptyr
patches: 1

resourceproto 1.2.0 Xorg ResourceProto protocol headers

Resource Extension defines a protocol that allows a client to query the X server about its usage of various resources.

https://www.x.org/wiki/
Part of GNU rest 0.8.0 RESTful web api query library

This library was designed to make it easier to access web services that claim to be "RESTful". It includes convenience wrappers for libsoup and libxml to ease remote use of the RESTful API.

http://www.gtk.org/
retroarch 1.6.7 Reference frontend for the libretro API

Libretro is a simple but powerful development interface that allows for the easy creation of emulators, games and multimedia applications that can plug straight into any libretro-compatible frontend. RetroArch is the official reference frontend for the libretro API, currently used by most as a modular multi-system game/emulator system.

https://www.libretro.com/
retux 1.3.5 Action platformer game

ReTux is an action platformer loosely inspired by the Mario games, utilizing the art assets from the SuperTux project.

http://retux.nongnu.org
rev-plugins 0.7.1 LADSPA reverb plugin

This package provides a stereo reverb LADSPA plugin based on the well-known greverb.

http://kokkinizita.linuxaudio.org
rfkill 0.5 Tool for enabling and disabling wireless devices

rfkill is a simple tool for accessing the rfkill device interface, which is used to enable and disable wireless networking devices, typically WLAN, Bluetooth and mobile broadband.

non-copyleft (This is a lax, non-copyleft free software license. Check the URI for details. See COPYING in the distribution.)
https://wireless.wiki.kernel.org/en/users/Documentation/rfkill
Part of GNU rhythmbox 3.4.1 Music player for GNOME

Rhythmbox is a music playing application for GNOME. It supports playlists, song ratings, and any codecs installed through gstreamer.

https://wiki.gnome.org/Apps/Rhythmbox
ribodiff 0.2.2 Detect translation efficiency changes from ribosome footprints

RiboDiff is a statistical tool that detects the protein translational efficiency change from Ribo-Seq (ribosome footprinting) and RNA-Seq data. It uses a generalized linear model to detect genes showing difference in translational profile taking mRNA abundance into account. It facilitates us to decipher the translational regulation that behave independently with transcriptional regulation.

http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/
ribotaper 1.3.1 Define translated ORFs using ribosome profiling data

Ribotaper is a method for defining translated open reading frames (ORFs) using ribosome profiling (ribo-seq) data. This package provides the Ribotaper pipeline.

https://ohlerlab.mdc-berlin.de/software/RiboTaper_126/
ripit 3.9.0 Command-line program to extract audio CDs
ripperx 2.8.0 GTK program to rip and encode CD audio tracks

RipperX is a GTK program to rip CD audio tracks and encode them to the Ogg, MP3, or FLAC formats. Its goal is to be easy to use, requiring only a few mouse clicks to convert an entire album. It supports CDDB lookups for album and track information.

https://sourceforge.net/projects/ripperx/
patches: 1

ristretto 0.8.0 Fast and lightweight picture-viewer

The Ristretto Image Viewer is an application that can be used to view, and scroll through images. It can be used to run a slideshow of images, open images with other applications like an image-editor or configure an image as the desktop wallpaper.

http://docs.xfce.org/apps/ristretto/start
ritornello 1.0.0 Control-free peak caller for ChIP-seq data

Ritornello is a ChIP-seq peak calling algorithm based on signal processing that can accurately call binding events without the need to do a pair total DNA input or IgG control sample. It has been tested for use with narrow binding events such as transcription factor ChIP-seq.

https://github.com/KlugerLab/Ritornello
rkflashtool 0.0.0-1.094bd64 Tools for flashing Rockchip devices

Allows flashing of Rockchip based embedded linux devices. The list of currently supported devices is: RK2818, RK2918, RK2928, RK3026, RK3036, RK3066, RK312X, RK3168, RK3188, RK3288, RK3368.

https://github.com/linux-rockchip/rkflashtool
rlwrap 0.42 Wrapper to allow the editing of keyboard commands

Rlwrap is a 'readline wrapper', a small utility that uses the GNU readline library to allow the editing of keyboard input for any command. You should consider rlwrap especially when you need user-defined completion (by way of completion word lists) and persistent history, or if you want to program 'special effects' using the filter mechanism.

http://utopia.knoware.nl/~hlub/uck/rlwrap/
rmath-standalone 3.4.2 Standalone R math library

This package provides the R math library as an independent package.

http://www.r-project.org/
rng-tools 5 Random number generator daemon

Monitor a hardware random number generator, and supply entropy from that to the system kernel's /dev/random machinery.

https://sourceforge.net/projects/gkernel
roary 3.8.2 High speed stand-alone pan genome pipeline

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by the Prokka program) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. Roary is not intended for metagenomics or for comparing extremely diverse sets of genomes.

http://sanger-pathogens.github.io/Roary
rocksdb 5.2.1 Persistent key-value store for fast storage

RocksDB is a library that forms the core building block for a fast key-value server, especially suited for storing data on flash drives. It has a Log-Structured-Merge-Database (LSM) design with flexible tradeoffs between Write-Amplification-Factor (WAF), Read-Amplification-Factor (RAF) and Space-Amplification-Factor (SAF). It has multi-threaded compactions, making it specially suitable for storing multiple terabytes of data in a single database. RocksDB is partially based on LevelDB.

http://rocksdb.org/
patches: snippet

roffit 0.11-1.e5228388e Convert nroff files to HTML

Roffit is a program that reads an nroff file and outputs an HTML file. It is typically used to display man pages on a web site.

https://daniel.haxx.se/projects/roffit/
rofi 1.4.1 Application launcher

Rofi is a minimalist application launcher. It memorizes which applications you regularly use and also allows you to search for an application by name.

https://davedavenport.github.io/rofi/
rosegarden 17.04 Music composition and editing environment based around a MIDI sequencer

Rosegarden is a music composition and editing environment based around a MIDI sequencer that features a rich understanding of music notation and includes basic support for digital audio.

http://www.rosegardenmusic.com/
Part of GNU rottlog 0.72.2 Log rotation and management

GNU Rot[t]log is a program for managing log files. It is used to automatically rotate out log files when they have reached a given size or according to a given schedule. It can also be used to automatically compress and archive such logs. Rot[t]log will mail reports of its activity to the system administrator.

https://www.gnu.org/software/rottlog/
patches: snippet

rpcbind 0.2.4 Server to convert RPC program numbers into universal addresses

Rpcbind is a server that converts RPC program numbers into universal addresses.

http://rpcbind.sourceforge.net/
patches: 1

rpm 4.13.0.1 The RPM Package Manager

The RPM Package Manager (RPM) is a command-line driven package management system capable of installing, uninstalling, verifying, querying, and updating computer software packages. Each software package consists of an archive of files along with information about the package like its version, a description. There is also a library permitting developers to manage such transactions from C or Python.

http://www.rpm.org/
rrdtool 1.4.8 Time-series data storage and display system

The Round Robin Database Tool (RRDtool) is a system to store and display time-series data (e.g. network bandwidth, machine-room temperature, server load average). It stores the data in Round Robin Databases (RRDs), a very compact way that will not expand over time. RRDtool processes the extracted data to enforce a certain data density, allowing for useful graphical representation of data values.

http://oss.oetiker.ch/rrdtool/
rsem 1.2.20 Estimate gene expression levels from RNA-Seq data

RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides a user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, it can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.

http://deweylab.biostat.wisc.edu/rsem/
patches: 1, snippet

rseqc 2.6.1 RNA-seq quality control package

RSeQC provides a number of modules that can comprehensively evaluate high throughput sequence data, especially RNA-seq data. Some basic modules inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, etc.

http://rseqc.sourceforge.net/
patches: snippet

rsnapshot 1.4.2 Deduplicating snapshot backup utility based on rsync

rsnapshot is a filesystem snapshot utility based on rsync. rsnapshot makes it easy to make periodic snapshots of local machines, and remote machines over SSH. To reduce the disk space required for each backup, rsnapshot uses hard links to deduplicate identical files.

http://rsnapshot.org
rsound 1.1 Networked audio system

RSound allows you to send audio from an application and transfer it directly to a different computer on your LAN network. It is an audio daemon with a much different focus than most other audio daemons.

http://themaister.net/rsound.html
rss-bridge 2017-08-03 Generate Atom feeds for social networking websites

rss-bridge generates Atom feeds for social networking websites lacking feeds. Supported websites include Facebook, Twitter, Instagram and YouTube.

https://github.com/RSS-Bridge/rss-bridge
rsync 3.1.2 Remote (and local) file copying tool

Rsync is a fast and versatile file copying tool. It can copy locally, to/from another host over any remote shell, or to/from a remote rsync daemon. Its delta-transfer algorithm reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination.

http://rsync.samba.org/
rtl-sdr 0.5.3 Software defined radio driver for Realtek RTL2832U

DVB-T dongles based on the Realtek RTL2832U can be used as a cheap software defined radio, since the chip allows transferring the raw I/Q samples to the host. rtl-sdr provides drivers for this purpose.

https://osmocom.org/projects/sdr/wiki/rtl-sdr
rtmidi 2.1.0 Cross-platform MIDI library for C++

RtMidi is a set of C++ classes (RtMidiIn, RtMidiOut, and API specific classes) that provide a common cross-platform API for realtime MIDI input/output.

https://github.com/powertab/rtmidi
rtorrent 0.9.6 BitTorrent client with ncurses interface

rTorrent is a BitTorrent client with an ncurses interface. It supports full encryption, DHT, PEX, and Magnet Links. It can also be controlled via XML-RPC over SCGI.

https://github.com/rakshasa/rtorrent
rubber 1.1 Wrapper for LaTeX and friends

Rubber is a program whose purpose is to handle all tasks related to the compilation of LaTeX documents. This includes compiling the document itself, of course, enough times so that all references are defined, and running BibTeX to manage bibliographic references. Automatic execution of dvips to produce PostScript documents is also included, as well as usage of pdfLaTeX to produce PDF documents.

https://launchpad.net/rubber
rubberband 1.8.1 Audio time-stretching and pitch-shifting library

Rubber Band is a library and utility program that permits changing the tempo and pitch of an audio recording independently of one another.

http://breakfastquay.com/rubberband/
ruby 2.3.5 Programming language interpreter

Ruby is a dynamic object-oriented programming language with a focus on simplicity and productivity.

https://ruby-lang.org
patches: snippet

ruby 2.4.2 Programming language interpreter

Ruby is a dynamic object-oriented programming language with a focus on simplicity and productivity.

https://ruby-lang.org
patches: snippet

ruby 2.2.8 Programming language interpreter

Ruby is a dynamic object-oriented programming language with a focus on simplicity and productivity.

https://ruby-lang.org
ruby 2.1.10 Programming language interpreter

Ruby is a dynamic object-oriented programming language with a focus on simplicity and productivity.

https://ruby-lang.org
ruby 1.8.7-p374 Programming language interpreter

Ruby is a dynamic object-oriented programming language with a focus on simplicity and productivity.

https://ruby-lang.org
ruby-activesupport 5.1.4 Ruby on Rails utility library

ActiveSupport is a toolkit of support libraries and Ruby core extensions extracted from the Rails framework. It includes support for multibyte strings, internationalization, time zones, and testing.

http://www.rubyonrails.org
ruby-ae 1.8.2 Assertions library

Assertive Expressive (AE) is an assertions library specifically designed for reuse by other test frameworks.

http://rubyworks.github.io/ae
ruby-afm 0.2.2 Read Adobe Font Metrics (afm) files

This library provides methods to read Adobe Font Metrics (afm) files and use the data therein.

https://github.com/halfbyte/afm
ruby-ansi 1.5.0 ANSI escape code related libraries

This package is a collection of ANSI escape code related libraries enabling ANSI colorization and stylization of console output. Included in the library are the Code module, which defines ANSI codes as constants and methods, a Mixin module for including color methods, a Logger, a ProgressBar, and a String subclass. The library also includes a Terminal module which provides information about the current output device.

http://rubyworks.github.io/ansi
ruby-arel 8.0.0 SQL AST manager for Ruby

Arel is an SQL Abstract Syntax Tree (AST) manager for Ruby. It simplifies the generation of complex SQL queries and adapts to various relational database implementations.

https://github.com/rails/arel
ruby-ascii85 1.0.2 Encode and decode Ascii85 binary-to-text encoding

This library provides methods to encode and decode Ascii85 binary-to-text encoding. The main modern use of Ascii85 is in PostScript and Portable Document Format (PDF) file formats.

https://github.com/datawraith/ascii85gem
ruby-atoulme-antwrap 0.7.5 Ruby wrapper for the Ant build tool

Antwrap is a Ruby module that wraps the Apache Ant build tool. Antwrap can be used to invoke Ant tasks from a Ruby or a JRuby script.

http://rubyforge.org/projects/antwrap/
ruby-atoulme-saikuro 1.2.1 Cyclomatic complexity analyzer

Saikuro is a Ruby cyclomatic complexity analyzer. When given Ruby source code Saikuro will generate a report listing the cyclomatic complexity of each method found. In addition, Saikuro counts the number of lines per method and can generate a listing of the number of tokens on each line of code.

http://www.github.com/atoulme/Saikuro
ruby-bacon 1.2.0 Small RSpec clone

Bacon is a small RSpec clone providing all essential features.

https://github.com/chneukirchen/bacon
ruby-bio-commandeer 0.4.0 Simplified running of shell commands from within Ruby

Bio-commandeer provides an opinionated method of running shell commands from within Ruby. The advantage of bio-commandeer over other methods of running external commands is that when something goes wrong, messages printed to the STDOUT and STDERR streams are reported, giving extra detail to ease debugging.

https://github.com/wwood/bioruby-commandeer
ruby-bio-kseq 0.0.2 Ruby bindings for the kseq.h FASTA/Q parser

Bio::Kseq provides ruby bindings to the kseq.h FASTA and FASTQ parsing code. It provides a fast iterator over sequences and their quality scores.

https://github.com/gusevfe/bio-kseq
ruby-bio-logger 1.0.1 Log4r wrapper for Ruby

Bio-logger is a wrapper around Log4r adding extra logging features such as filtering and fine grained logging.

https://github.com/pjotrp/bioruby-logger-plugin
ruby-blankslate 3.1.3 Abstract base class with no predefined methods

BlankSlate provides an abstract base class with no predefined methods (except for __send__ and __id__). BlankSlate is useful as a base class when writing classes that depend upon method_missing (e.g. dynamic proxies).

https://github.com/masover/blankslate
ruby-brass 1.2.1 Basic foundational assertions framework

BRASS (Bare-Metal Ruby Assertion System Standard) is a basic foundational assertions framework for other assertion and test frameworks to make use of.

http://rubyworks.github.io/brass
ruby-builder 3.2.3 Ruby library to create structured data

Builder provides a number of builder objects that make it easy to create structured data. Currently the following builder objects are supported: XML Markup and XML Events.

https://github.com/jimweirich/builder
ruby-byebug 9.0.6 Debugger for Ruby 2

Byebug is a Ruby 2 debugger implemented using the Ruby 2 TracePoint C API for execution control and the Debug Inspector C API for call stack navigation. The core component provides support that front-ends can build on. It provides breakpoint handling and bindings for stack frames among other things and it comes with a command line interface.

https://github.com/deivid-rodriguez/byebug
ruby-ci-reporter 2.0.0 Generate XML reports of runs test

CI::Reporter is an add-on to Ruby testing frameworks that allows you to generate XML reports of your test runs. The resulting files can be read by a continuous integration system that understands Ant's JUnit report format.

https://github.com/nicksieger/ci_reporter
ruby-clap 1.0.0 Command line argument parsing for simple applications

Clap provides command line argument parsing features. It covers the simple case of executing code based on the flags or parameters passed.

https://github.com/djanowski/cutest
ruby-code-statistics 0.2.13 Port of the rails 'rake stats' method

This gem is a port of the rails 'rake stats' method so it can be made more robust and work for non rails projects.

http://github.com/danmayer/code_statistics
ruby-coderay 1.1.2 Ruby syntax highlighting library

Coderay is a Ruby library that provides syntax highlighting for select languages.

http://coderay.rubychan.de
ruby-concurrent 1.0.5 Concurrency tools for Ruby

This library provides modern concurrency tools including agents, futures, promises, thread pools, actors, supervisors, and more. It is inspired by Erlang, Clojure, Go, JavaScript, actors and classic concurrency patterns.

http://www.concurrent-ruby.com
patches: 1, 2

ruby-connection-pool 2.2.1 Generic connection pool for Ruby

Connection_pool provides a generic connection pooling interface for Ruby programs.

https://github.com/mperham/connection_pool
ruby-crass 1.0.2 Pure Ruby CSS parser

Crass is a pure Ruby CSS parser based on the CSS Syntax Level 3 spec.

https://github.com/rgrove/crass/
ruby-cucumber-core 2.0.0 Core library for the Cucumber BDD app

Cucumber is a tool for running automated tests written in plain language. Because they're written in plain language, they can be read by anyone on your team. Because they can be read by anyone, you can use them to help improve communication, collaboration and trust on your team.

https://cucumber.io/
ruby-cutest 1.2.2 Run tests in separate processes

Cutest runs tests in separate processes to avoid shared state.

https://github.com/djanowski/cutest
ruby-daemons 1.2.4 Daemonize Ruby programs

Daemons provides a way to wrap existing Ruby scripts to be run as a daemon and to be controlled by simple start/stop/restart commands.

https://github.com/thuehlinger/daemons
ruby-debug-inspector 0.0.3 Ruby wrapper for the MRI 2.0 debug_inspector API

This package provides a Ruby wrapper for the MRI 2.0 debug_inspector API.

https://github.com/banister/debug_inspector
ruby-diff-lcs 1.3 Compute the difference between two Enumerable sequences

Diff::LCS computes the difference between two Enumerable sequences using the McIlroy-Hunt longest common subsequence (LCS) algorithm. It includes utilities to create a simple HTML diff output format and a standard diff-like tool.

https://github.com/halostatue/diff-lcs
ruby-docile 1.1.5 Ruby EDSL helper library

Docile is a Ruby library that provides an interface for creating embedded domain specific languages (EDSLs) that manipulate existing Ruby classes.

https://ms-ati.github.io/docile/
ruby-domain-name 0.5.20170404 Domain name manipulation library

domain_name is a Domain name manipulation library. It parses a domain name ready for extracting the registered domain and TLD (Top Level Domain). It can also be used for cookie domain validation based on the Public Suffix List.

https://github.com/knu/ruby-domain_name
ruby-eventmachine 1.2.5 Single-threaded network event framework for Ruby

EventMachine implements a single-threaded engine for arbitrary network communications. EventMachine wraps all interactions with sockets, allowing programs to concentrate on the implementation of network protocols. It can be used to create both network servers and clients.

http://rubyeventmachine.com
ruby-ffi 1.9.18 Ruby foreign function interface library

Ruby-FFI is a Ruby extension for programmatically loading dynamic libraries, binding functions within them, and calling those functions from Ruby code. Moreover, a Ruby-FFI extension works without changes on Ruby and JRuby.

http://wiki.github.com/ffi/ffi
ruby-fivemat 1.3.5 Each test file given its own line of dots

Fivemat is a MiniTest/RSpec/Cucumber formatter that gives each test file its own line of dots during testing. It aims to provide test output that is neither too verbose nor too minimal.

https://github.com/tpope/fivemat
ruby-formatador 0.2.5 Ruby library to format text on stdout

Formatador is a Ruby library to format text printed to the standard output stream.

https://github.com/geemus/formatador
ruby-gem-hadar 1.9.1 Library for the development of Ruby gems

This library contains some useful functionality to support the development of Ruby gems.

https://github.com/flori/gem_hadar
ruby-gettext 3.1.7 GNU gettext-like program for Ruby

Gettext is a GNU gettext-like program for Ruby. The catalog file (po-file) used is the same as that used by GNU gettext, allowing you to use GNU gettext tools for maintenance.

http://ruby-gettext.github.com/
ruby-gherkin 4.1.3 Gherkin parser for Ruby

Gherkin is a parser and compiler for the Gherkin language. It is intended be used by all Cucumber implementations to parse '.feature' files.

https://github.com/cucumber/gherkin3
ruby-git 1.3.0 Ruby wrappers for Git

Ruby/Git is a Ruby library that can be used to create, read and manipulate Git repositories by wrapping system calls to the git binary.

https://github.com/schacon/ruby-git
ruby-guard 2.13.0 Tool to handle events on file system modifications

Guard is a command line tool to easily handle events on file system modifications. Guard automates various tasks by running custom rules whenever file or directories are modified.

http://guardgem.org/
ruby-hashery 2.1.2 Hash-like classes with extra features

The Hashery is a tight collection of Hash-like classes. Included are the auto-sorting Dictionary class, the efficient LRUHash, the flexible OpenHash and the convenient KeyHash. Nearly every class is a subclass of the CRUDHash which defines a CRUD (Create, Read, Update and Delete) model on top of Ruby's standard Hash making it possible to subclass and augment to fit any specific use case.

http://rubyworks.github.io/hashery
ruby-highline 1.7.8 HighLine helps you build command-line interfaces

HighLine provides a high-level IO library that provides validation, type conversion, and more for command-line interfaces. HighLine also includes a menu system for providing multiple options to the user.

https://github.com/JEG2/highline
ruby-hoe 3.16.0 Ruby project management helper

Hoe is a rake/rubygems helper for project Rakefiles. It helps manage, maintain, and release projects and includes a dynamic plug-in system allowing for easy extensibility. Hoe ships with plug-ins for all the usual project tasks including rdoc generation, testing, packaging, deployment, and announcement.

http://www.zenspider.com/projects/hoe.html
ruby-hoe-git 1.6.0 Hoe plugins for tighter Git integration

This package provides a set of Hoe plugins for tighter Git integration. It provides tasks to automate release tagging and pushing and changelog generation.

https://github.com/jbarnette/hoe-git
ruby-http-cookie 1.0.3 Handle HTTP Cookies based on RFC 6265

HTTP::Cookie is a Ruby library to handle HTTP Cookies based on RFC 6265. It has been designed with security, standards compliance and compatibility in mind, to behave just the same as today's major web browsers. It has built-in support for the legacy cookies.txt and cookies.sqlite formats of Mozilla Firefox.

https://github.com/sparklemotion/http-cookie
ruby-httpclient 2.8.3 Make HTTP requests with support for HTTPS, Cookies, authentication and more

The httpclient ruby library provides functionality related to HTTP. Compared to the net/http library, {httpclient

https://github.com/nahi/httpclient
ruby-i18n 0.7.0 Internationalization library for Ruby

Ruby i18n is an internationalization and localization solution for Ruby programs. It features translation and localization, interpolation of values to translations, pluralization, customizable transliteration to ASCII, flexible defaults, bulk lookup, lambdas as translation data, custom key/scope separator, custom exception handlers, and an extensible architecture with a swappable backend.

https://github.com/svenfuchs/i18n
ruby-instantiator 0.0.6 Instantiate an arbitrary Ruby class

Instantiator lets you instantiate an arbitrary Ruby class without knowing anything about the constructor.

https://github.com/floehopper/instantiator
ruby-introspection 0.0.4 Dynamic inspection of the method hierarchy on a Ruby object

Introspection provides tools to inspect the hierarchy of method definitions on a Ruby object.

https://github.com/floehopper/introspection
ruby-json 2.1.0 JSON library for Ruby

This Ruby library provides a JSON implementation written as a native C extension.

http://json-jruby.rubyforge.org/
ruby-json-pure 2.1.0 JSON implementation in pure Ruby

This package provides a JSON implementation written in pure Ruby.

http://flori.github.com/json
ruby-lemon 0.9.1 Test framework correlating code structure and test unit

Lemon is a unit testing framework that enforces highly formal case-to-class and unit-to-method test construction. This enforcement can help focus concern on individual units of behavior.

http://rubyworks.github.io/lemon
ruby-libxml 3.0.0 Ruby bindings for GNOME Libxml2

The Libxml-Ruby project provides Ruby language bindings for the GNOME Libxml2 XML toolkit.

http://xml4r.github.com/libxml-ruby
ruby-listen 3.1.5 Listen to file modifications

The Listen gem listens to file modifications and notifies you about the changes.

https://github.com/guard/listen
ruby-locale 2.1.2 Ruby library providing basic localization APIs

Ruby-Locale is the pure ruby library which provides basic APIs for localization.

https://github.com/ruby-gettext/locale
ruby-log4r 1.1.10 Flexible logging library for Ruby

Comprehensive and flexible logging library written in Ruby for use in Ruby programs. It features a hierarchical logging system of any number of levels, custom level names, logger inheritance, multiple output destinations per log event, execution tracing, custom formatting, thread safteyness, XML and YAML configuration, and more.

http://log4r.rubyforge.org/
ruby-lumberjack 1.0.12 Logging utility library for Ruby

Lumberjack is a simple logging utility that can be a drop in replacement for Logger or ActiveSupport::BufferedLogger. It provides support for automatically rolling log files even with multiple processes writing the same log file.

https://github.com/bdurand/lumberjack
ruby-mail 2.6.6 Mail library for Ruby

Mail is an internet library for Ruby that is designed to handle email generation, parsing and sending. The purpose of this library is to provide a single point of access to handle all email functions, including sending and receiving emails. All network type actions are done through proxy methods to Net::SMTP, Net::POP3 etc.

Mail has been designed with a very simple object oriented system that really opens up the email messages you are parsing, if you know what you are doing, you can fiddle with every last bit of your email directly.

https://github.com/mikel/mail
ruby-metaclass 0.0.4 Ruby library adding metaclass method to all objects

Metaclass is a Ruby library adding a metaclass method to all Ruby objects.

https://github.com/floehopper/metaclass
ruby-method-source 0.9.0 Retrieve the source code for Ruby methods

Method_source retrieves the source code for Ruby methods. Additionally, it can extract source code from Proc and Lambda objects or just extract comments.

https://github.com/banister/method_source
ruby-mime-types 3.1 Library and registry for MIME content type definitions

The mime-types library provides a library and registry for information about Multipurpose Internet Mail Extensions (MIME) content type definitions. It can be used to determine defined filename extensions for MIME types, or to use filename extensions to look up the likely MIME type definitions.

https://github.com/mime-types/ruby-mime-types
ruby-mime-types-data 3.2016.0521 Registry for information about MIME media type definitions

mime-types-data provides a registry for information about Multipurpose Internet Mail Extensions (MIME) media type definitions. It can be used with the Ruby mime-types library or other software to determine defined filename extensions for MIME types, or to use filename extensions to look up the likely MIME type definitions.

https://github.com/mime-types/mime-types-data/
ruby-mini-portile 0.6.2 Ports system for Ruby developers

Mini-portile is a port/recipe system for Ruby developers. It provides a standard way to compile against specific versions of libraries to reproduce user environments.

https://github.com/flavorjones/mini_portile
ruby-mini-portile 2.2.0 Ports system for Ruby developers

Mini-portile is a port/recipe system for Ruby developers. It provides a standard way to compile against specific versions of libraries to reproduce user environments.

https://github.com/flavorjones/mini_portile
ruby-minitar 0.5.4-1.e25205ec Ruby library and utility for handling tar archives

Archive::Tar::Minitar is a pure-Ruby library and command-line utility that provides the ability to deal with POSIX tar archive files.

http://www.github.com/atoulme/minitar
ruby-minitest 4.7.5 Small test suite library for Ruby

Minitest provides a complete suite of Ruby testing facilities supporting TDD, BDD, mocking, and benchmarking.

https://github.com/seattlerb/minitest
ruby-minitest 5.10.3 Small test suite library for Ruby

Minitest provides a complete suite of Ruby testing facilities supporting TDD, BDD, mocking, and benchmarking.

https://github.com/seattlerb/minitest
ruby-minitest-bacon 1.0.3 Bacon compatibility library for minitest

Minitest-bacon extends minitest with bacon-like functionality, making it easier to migrate test suites from bacon to minitest.

https://github.com/seattlerb/minitest-bacon
ruby-minitest-bonus-assertions 3.0 Bonus assertions for Minitest

Minitest bonus assertions provides extra MiniTest assertions. For instance, it provides assert_true, assert_false and assert_set_equal.

https://github.com/halostatue/minitest-bonus-assertions
ruby-minitest-focus 1.1.2 Allows a few specific tests to be focused on

minitest-focus gives the ability focus on a few tests with ease without having to use command-line arguments. It introduces a focus class method for use in testing classes, specifying that the next defined test is to be run.

https://github.com/seattlerb/minitest-focus
ruby-minitest-hooks 1.4.1 Hooks for the minitest framework

Minitest-hooks adds around, before_all, after_all, around_all hooks for Minitest. This allows, for instance, running each suite of specs inside a database transaction, running each spec inside its own savepoint inside that transaction. This can significantly speed up testing for specs that share expensive database setup code.

https://github.com/jeremyevans/minitest-hooks
ruby-minitest-moar 0.0.4 Extra features and changes to MiniTest

MiniTest Moar add some additional features and changes some default behaviours in MiniTest. For instance, Moar replaces the MiniTest Object#stub with a global stub method.

https://github.com/dockyard/minitest-moar
ruby-minitest-pretty-diff 0.1-1.11f32e93 Pretty-print hashes and arrays in MiniTest

minitest-pretty_diff monkey-patches MiniTest::Assertions#mu_pp to pretty-print hashes and arrays before diffing them. This makes it easier to spot differences between nested structures when tests fail.

https://github.com/adammck/minitest-pretty_diff
ruby-minitest-rg 5.2.0 Coloured output for Minitest

minitest-rg changes the colour of the output from Minitest.

http://blowmage.com/minitest-rg
ruby-minitest-sprint 1.1.0 Fast test suite runner for minitest

Minitest-sprint is a test runner for minitest that makes it easier to re-run individual failing tests.

https://github.com/seattlerb/minitest-sprint
ruby-minitest-tu-shim 1.3.3 Adapter library between minitest and test/unit

This library bridges the gap between the small and fast minitest and Ruby's large and slower test/unit.

https://rubygems.org/gems/minitest_tu_shim
ruby-mocha 1.1.0 Mocking and stubbing library for Ruby

Mocha is a mocking and stubbing library with JMock/SchMock syntax, which allows mocking and stubbing of methods on real (non-mock) classes.

http://gofreerange.com/mocha/docs
ruby-multi-json 1.12.2 Common interface to multiple JSON libraries for Ruby

This package provides a common interface to multiple JSON libraries, including Oj, Yajl, the JSON gem (with C-extensions), the pure-Ruby JSON gem, NSJSONSerialization, gson.rb, JrJackson, and OkJson.

http://github.com/intridea/multi_json
ruby-multipart-post 2.0.0 Multipart POST library for Ruby

Multipart-Post Adds multipart POST capability to Ruby's net/http library.

https://github.com/nicksieger/multipart-post
ruby-nenv 0.3.0 Ruby interface for modifying the environment

Nenv provides a convenient wrapper for Ruby's ENV to modify and inspect the environment.

https://github.com/e2/nenv
ruby-net-http-digest-auth 1.4.1 RFC 2617 HTTP digest authentication library

This library implements HTTP's digest authentication scheme based on RFC 2617. This enables the use of the digest authentication scheme instead of the more insecure basic authentication scheme.

https://github.com/drbrain/net-http-digest_auth
ruby-net-http-persistent 3.0.0 Persistent HTTP connection manager

Net::HTTP::Persistent manages persistent HTTP connections using Net::HTTP, supporting reconnection and retry according to RFC 2616.

https://github.com/drbrain/net-http-persistent
ruby-net-ssh 4.1.0 Ruby implementation of the SSH2 client protocol

Net::SSH is a pure-Ruby implementation of the SSH2 client protocol. It allows you to write programs that invoke and interact with processes on remote servers, via SSH2.

https://github.com/net-ssh/net-ssh
ruby-netrc 0.11.0 Library to read and update netrc files

This library can read and update netrc files, preserving formatting including comments and whitespace.

https://github.com/geemus/netrc
ruby-nokogiri 1.8.0 HTML, XML, SAX, and Reader parser for Ruby

Nokogiri (鋸) parses and searches XML/HTML, and features both CSS3 selector and XPath 1.0 support.

http://www.nokogiri.org/
ruby-nokogiri-diff 0.2.0-1.a38491e4 Calculate the differences between two XML/HTML documents

Nokogiri::Diff adds the ability to calculate the differences (added or removed nodes) between two XML/HTML documents.

https://github.com/postmodern/nokogiri-diff
ruby-nokogumbo 1.4.7-1.fb51ff29 Ruby bindings to the Gumbo HTML5 parser

Nokogumbo allows a Ruby program to invoke the Gumbo HTML5 parser and access the result as a Nokogiri parsed document.

https://github.com/rubys/nokogumbo/
ruby-notiffany 0.1.1 Wrapper libray for notification libraries

Notiffany is a Ruby wrapper libray for notification libraries such as Libnotify.

https://github.com/guard/notiffany
ruby-options 2.3.2 Ruby library to parse options from *args cleanly

The options library helps with parsing keyword options in Ruby functions.

https://github.com/ahoward/options
ruby-orderedhash 0.0.6 Ruby library providing an order-preserving hash

Orderedhash is a Ruby library providing a hash implementation that preserves the order of items and features some array-like extensions.

http://codeforpeople.com/lib/ruby/orderedhash/
ruby-ox 2.6.0 Optimized XML library for Ruby

Optimized XML (Ox) is a fast XML parser and object serializer for Ruby written as a native C extension. It was designed to be an alternative to Nokogiri and other Ruby XML parsers for generic XML parsing and as an alternative to Marshal for Object serialization.

http://www.ohler.com/ox