Packages — R (Page 1 of 7)

r 3.4.3 — Environment for statistical computing and graphics

This is a GNU package.

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.

r-acepack 1.4.1 — Functions for regression transformations

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

r-acsnminer — 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.

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.

r-ade4 1.7-10 — 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.

r-affy 1.56.0 — Methods for affymetrix oligonucleotide arrays

This package contains functions for exploratory oligonucleotide array analysis.

r-affyio 1.48.0 — 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.

r-annotate 1.56.1 — Annotation for microarrays

This package provides R environments for the annotation of microarrays.

r-annotationdbi 1.40.0 — Annotation database interface

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

r-annotationfilter 1.2.0 — 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.

r-annotationforge 1.20.0 — 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.

r-annotationhub 2.10.1 — 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.

r-ape 5.0 — 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.

r-aroma-light 3.8.0 — 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.

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.

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.

r-backports 1.1.2 — 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.

r-bamsignals 1.10.0 — 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.

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.

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.

r-batchjobs 1.7 — 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.

r-bbmisc 1.11 — Miscellaneous functions for R package development

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

r-bbmle 1.0.20 — Tools for General Maximum Likelihood Estimation

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

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.

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.

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).

r-bigmemory 4.5.31 — 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.

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.

r-bindr 0.1 — Parametrized active bindings

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

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.

r-biobase 2.38.0 — Base functions for Bioconductor

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

r-bioccheck 1.14.0 — 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.

r-biocgenerics 0.24.0 — S4 generic functions for Bioconductor

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

r-biocinstaller 1.28.0 — Install Bioconductor packages

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

r-biocparallel 1.12.0 — Bioconductor facilities for parallel evaluation

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

r-biocstyle 2.6.1 — Bioconductor formatting styles

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

r-biocviews 1.46.0 — 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.

r-biomart 2.34.1 — Interface to BioMart databases

biomaRt provides an interface to a growing collection of databases implementing the 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.

r-biostrings 2.46.0 — 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.

r-biovizbase 1.26.0 — Basic graphic utilities for visualization of genomic data

The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.

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.

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.

r-bitops 1.0-6 — Bitwise operations

This package provides functions for bitwise operations on integer vectors.

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.

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.

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.

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.

r-broom 0.4.3 — Convert statistical analysis objects into tidy data frames

This package provides tools to convert statistical analysis objects from R into tidy data frames, so that they can more easily be combined, reshaped and otherwise processed with tools like dplyr, tidyr and ggplot2. The package provides three S3 generics: tidy, which summarizes a model's statistical findings such as coefficients of a regression; augment, which adds columns to the original data such as predictions, residuals and cluster assignments; and glance, which provides a one-row summary of model-level statistics.

r-bsgenome 1.46.0 — 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

r-car 2.1-6 — Companion to applied regression

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

r-caret 6.0-78 — Classification and regression training

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

r-category 2.44.0 — Category analysis

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

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.

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.

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.

r-checkmate 1.8.5 — 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.

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.

r-chipseq 1.28.0 — Package for analyzing ChIPseq data

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

r-chron 2.3-51 — Chronological R objects which can handle dates and times

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

r-circlize 0.4.2 — 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.

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.

r-cli 1.0.0 — Helpers for developing command line interfaces

This package provides a suite of tools designed to build attractive command line interfaces (CLIs). It includes tools for drawing rules, boxes, trees, and Unicode symbols with ASCII alternatives.

r-cluster 2.0.6 — Methods for cluster analysis

This package provides methods for cluster analysis. It is a much extended version of the original from Peter Rousseeuw, Anja Struyf and Mia Hubert, based on Kaufman and Rousseeuw (1990) "Finding Groups in Data".

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.

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.

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.

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.

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.

r-complexheatmap 1.17.1 — Making Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

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.

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.

r-copynumber 1.18.0 — Segmentation of single- and multi-track copy number data

This package segments single- and multi-track copy number data by a penalized least squares regression method.

r-copywriter 2.10.0 — 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.

r-corrplot 0.84 — Visualization of a correlation matrix

This package provides a graphical display of a correlation matrix or general matrix. It also contains some algorithms to do matrix reordering. In addition, corrplot is good at details, including choosing color, text labels, color labels, layout, etc.

r-cowplot 0.9.2 — 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.

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.

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.

r-curl 3.1 — 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.

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.

r-data-table 1.10.4-3 — 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.

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.

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.

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.

r-delayedarray 0.4.1 — 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.

r-dendextend 1.6.0 — 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.

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.

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.

r-deseq 1.30.0 — 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.

r-deseq2 1.18.1 — 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.

r-devtools 1.13.4 — Tools to make developing R packages easier

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

r-dexseq 1.24.2 — 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.