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 version||Package details|
|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.
|r-acepack 1.4.1||Functions for regression transformations|
|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.
|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 1.7-8||Multivariate data analysis and graphical display|
|r-affy 1.54.0||Methods for affymetrix oligonucleotide arrays|
|r-affyio 1.46.0||Tools for parsing Affymetrix data files|
|r-annotate 1.54.0||Annotation for microarrays|
|r-annotationdbi 1.38.2||Annotation database interface|
|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
|r-annotationforge 1.18.1||Code for building annotation database packages|
|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.
|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.
|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.
|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 1.1.1||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.
|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.
|r-base64 2.0||Base64 encoder and decoder|
|r-base64enc 0.1-3||Tools for Base64 encoding|
|r-batchjobs 1.6||Batch computing with R|
|r-bbmisc 1.11||Miscellaneous functions for R package development|
|r-bbmle 1.0.19||Tools for General Maximum Likelihood Estimation|
|r-beeswarm 0.2.3||Implementation of bee swarm plots|
|r-bh 1.65.0-1||R package providing subset of Boost headers|
|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 4.5.19||Manage large matrices with shared memory or memory-mapped files|
|r-bigmemory-sri 0.1.3||Shared resource interface for the bigmemory package|
|r-bindr 0.1||Parametrized active bindings|
|r-bindrcpp 0.2||Rcpp interface to active bindings|
|r-biobase 2.36.2||Base functions for Bioconductor|
|r-bioccheck 1.12.0||Executes Bioconductor-specific package checks|
|r-biocgenerics 0.22.0||S4 generic functions for Bioconductor|
|r-biocinstaller 1.26.0||Install Bioconductor packages|
|r-biocparallel 1.10.1||Bioconductor facilities for parallel evaluation|
|r-biocstyle 2.4.1||Bioconductor formatting styles|
|r-biocviews 1.44.0||Bioconductor package categorization helper|
|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.
|r-biostrings 2.44.2||String objects and algorithms for biological sequences|
|r-bit 1.1-12||Class for vectors of 1-bit booleans
This package provides bitmapped vectors of booleans (no
|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
|r-bitops 1.0-6||Bitwise operations|
|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|
|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|
|r-bsgenome 1.44.0||Infrastructure for Biostrings-based genome data packages|
|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|
|r-car 2.1-5||Companion to applied regression|
|r-caret 6.0-77||Classification and regression training|
|r-category 2.42.1||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|
|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 1.8.4||Fast and versatile argument checks|
|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 1.26.0||Package for analyzing ChIPseq data|
|r-chron 2.3-50||Chronological R objects which can handle dates and times|
|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.
|r-class 7.3-14||R functions for classification|
|r-cluster 2.0.6||Methods for data cluster analysis|
|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|
|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-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-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.
|r-cowplot 0.8.0||Streamlined plot theme and plot annotations for ggplot2|
|r-crayon 1.3.4||Colored terminal output for R
|r-crosstalk 1.0.0||Inter-widget interactivity for HTML widgets|
|r-curl 2.8.1||HTTP client for R
|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||Enhanced version of data.frame R object
The R package
|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
|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 0.2.7||Delayed operations on array-like objects
Wrapping an array-like object (typically an on-disk object) in a
|r-dendextend 1.5.2||Extending 'dendrogram' functionality in R
This package offers a set of functions for extending
|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|
|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.
|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.
|r-devtools 1.13.3||Tools to make developing R packages easier|
|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.
|r-dichromat 2.0-0||Color schemes for dichromats|
|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.
|r-dimred 0.1.0||Framework for dimensionality reduction|
|r-diptest 0.75-7||Hartigan's dip test statistic for unimodality|
|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.
|r-dnacopy 1.50.1||Implementation of a circular binary segmentation algorithm|
|r-domc 1.3.4||Foreach parallel adaptor for the 'parallel' package|
|r-doparallel 1.0.11||Foreach parallel adaptor for the 'parallel' package|
|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.
|r-drr 0.0.2||Dimensionality reduction via regression|
|r-dynamictreecut 1.63-1||Detect clusters in hierarchical clustering dendrograms
This package contains methods for the detection of clusters in hierarchical clustering dendrograms.
|r-e1071 1.6-8||Miscellaneous functions for probability theory|
|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.
|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.
|r-emdbook 1.3.9||Support functions and data for "Ecological Models and Data"|
|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.
|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.
|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.
|r-extremes 2.0-8||Extreme value analysis|
|r-fail 1.3||File abstraction interface layer (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:
|r-fastica 1.2-1||FastICA algorithms to perform ICA and projection pursuit|
|r-fastmatch 1.1-0||Fast match function
This package provides a fast
|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.
|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.
|r-ff 2.2-13||Memory-efficient storage of large data on disk and access functions|
|r-ffbase 0.12.3||Basic statistical functions for package 'ff'|
|r-fit-models 0.5-14||Compare fitted models
|r-fitdistrplus 1.0-9||Fitting a parametric distribution from data
This package extends the
|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.
|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.
|r-fnn 1.1||Fast nearest neighbor search algorithms and applications|
|r-foreach 1.4.3||Foreach looping construct for R
This package provides support for the
|r-foreign 0.8-69||Read data stored by other statistics software|
|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.
|r-formula 1.2-2||Extended model formulas
This package provides a new class
|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.
|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
|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
|r-gdata 2.18.0||Various R programming tools for data manipulation
This package provides various R programming tools for data manipulation, including:
|r-gdtools 0.1.6||Utilities for graphical rendering|
|r-genefilter 1.58.0||Filter genes from high-throughput experiments|
|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.
|r-genomationdata 1.6.0||Experimental data for use with the genomation package|
|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.
|r-genomeinfodbdata 0.99.0||Species and taxonomy ID look up tables for GenomeInfoDb|
|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.
|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.
|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.
|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
|r-getoptlong 0.1.6||Parsing command-line arguments and variable interpolation|
|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.
|r-ggbeeswarm 0.6.0||Categorical scatter (violin point) plots|
|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.
|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.
|r-ggthemes 3.4.0||Extra themes, scales and geoms for
This package provides extra themes and scales for
|r-git2r 0.19.0||Access Git repositories with R|
|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.
|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.
|r-globaloptions 0.0.12||Generate functions to get or set global options|
|r-glue 1.1.1||Interpreted string literals|
|r-go-db 3.4.0||Annotation maps describing the entire Gene Ontology|
|r-googlesheets 0.2.2||Manage Google spreadsheets from R|
|r-gostats 2.42.0||Tools for manipulating GO and microarrays|
|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.
|r-gplots 3.0.1||Various R programming tools for plotting data
This package provides various R programming tools for plotting data, including:
|r-graph 1.54.0||Handle graph data structures in R|
|r-gridbase 0.4-7||Integration of base and grid graphics|
|r-gridextra 2.3||Miscellaneous functions for "Grid" graphics|
|r-grohmm 1.10.0||GRO-seq analysis pipeline|
|r-gseabase 1.38.0||Gene set enrichment data structures and methods|
|r-gtable 0.2.0||R library to arrange grobs in tables|
|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
|r-hexbin 1.27.1-1||Hexagonal binning routines|
|r-highr 0.6||Syntax highlighting for R source code|
|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.
|r-hms 0.3||Pretty time of day|
|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.
|r-htmltools 0.3.6||R tools for HTML|
|r-htmlwidgets 0.9||HTML Widgets for R|
|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.
|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 (
|r-hwriter 1.3.2||Output R objects in HTML format|
|r-igraph 1.1.2||Network analysis and visualization|
|r-impute 1.50.0||Imputation for microarray data|
|r-inline 0.3.14||Functions to inline C, C++, Fortran function calls from R|
|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.
|r-ipred 0.9-6||Improved predictors|
|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
|r-irlba 2.2.1||Methods for eigendecomposition of large matrices|
|r-iterators 1.0.8||Iterator construct for R|
|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.
|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
|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|
|r-knitrbootstrap 1.0.1||Knitr bootstrap framework|
|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.
|r-labeling 0.3||Axis labeling algorithms|
|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.
|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.
|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.
|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.
|r-lava 1.5.1||Latent variable models|
|r-lazyeval 0.2.0||Lazy (non-standard) evaluation in R|
|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.
|r-limsolve 188.8.131.52||Solving linear inverse models
This package provides functions that:
It includes banded and tridiagonal linear systems. The package calls Fortran functions from LINPACK.
|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.
|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.
|r-lmtest 0.9-35||Testing linear regression models|
|r-locfit 1.5-9.1||Local regression, likelihood and density estimation|
|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.
|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.
|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."
|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.
|r-markdown 0.8||Markdown rendering for R|
|r-mass 7.3-47||Support functions and datasets for Venables and Ripley's MASS|
|r-matrix 1.2-11||Sparse and dense matrix classes and methods|
|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.
|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.
|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.
|r-memoise 1.1.0||Memoise functions for R|
|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.
|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
|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.
|r-mime 0.5||R package to map filenames to MIME types|
|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.
|r-minqa 1.2.4||Derivative-free optimization algorithms by quadratic approximation|
|r-mixtools 1.1.0||Tools for analyzing finite mixture models|
|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.
|r-modelmetrics 1.1.0||Rapid calculation of model metrics
Written in C++ using
|r-modeltools 0.2-21||Tools and classes for statistical models|
|r-motifrg 1.20.0||Discover motifs in high throughput sequencing data|
|r-msnbase 2.2.0||Base functions and classes for MS-based proteomics|
|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.
|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.
|r-munsell 0.4.3||Munsell colour system|
|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.
|r-mvtnorm 1.0-6||Package for multivariate normal and t-distributions|
|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.
|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.
|r-nlme 3.1-131||Linear and nonlinear mixed effects models|
|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.
|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.
|r-nnet 7.3-12||Feed-forward neural networks and multinomial log-linear models|
|r-numderiv 2016.8-1||Accurate numerical derivatives|
|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
|r-optparse 1.4.4||Command line option parser|
|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.
|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.
|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.
|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.
|r-pbapply 1.3-3||Adding progress bar to apply functions|
|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.
|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.
|r-pcapp 1.9-72||Robust PCA by projection pursuit|
|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).
|r-pheatmap 1.0.8||Pretty heatmaps|
|r-pkgconfig 2.0.1||Private configuration for R packages|
|r-pkgmaker 0.22||Package development utilities|
|r-plogr 0.1-1||R bindings for the plog C++ logging library|
|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.
|r-plotrix 3.6-6||Various plotting functions|
|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.
|r-png 0.1-7||Read and write PNG images|
|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.
|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.
|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.
|r-praise 1.0.0||Functions to praise users|
|r-preprocesscore 1.38.1||Collection of pre-processing functions|
|r-prettyunits 1.0.2||Pretty, human readable formatting of quantities|
|r-prodlim 1.6.1||Product-limit estimation for censored event history analysis|
|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.
|r-protgenerics 1.8.0||S4 generic functions for proteomics infrastructure|
|r-proto 1.0.0||Prototype object-based programming|
|r-proxy 0.4-17||Distance and similarity measures|
|r-pryr 0.1.2||Tools for computing on the R language|
|r-purrr 0.2.3||Functional programming tools|
|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.
|r-quadprog 1.5-5||Functions to solve quadratic programming problems|
|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.
|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.
|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).
|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
|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.
|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.
|r-r-utils 2.5.0||Various programming utilities|
|r-r4rna 0.1.4||Analysis framework for RNA secondary structure|
|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.
|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.
|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.
|r-rann 2.5.1||Fast nearest neighbour search|
|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.
|r-rbgl 1.52.0||Interface to the Boost graph library|
|r-rcas 1.3.4||RNA-centric annotation system|
|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
|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.
|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.
|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.
|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.
|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.
|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.
|r-readr 1.1.1||Read tabular data|
|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.
|r-registry 0.3||Infrastructure for R package registries|
|r-rematch 1.0.1||Match regular expressions with a nicer API|
|r-reshape 0.8.7||Flexibly reshape data|
|r-reshape2 1.4.2||Flexibly reshape data: a reboot of the "reshape" package|
|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.
|r-rhtslib 1.8.0||High-throughput sequencing library as an R package|
|r-rjson 0.2.15||JSON library for R|
|r-rlang 0.1.2||Functions for base types, core R and Tidyverse features|
|r-rmarkdown 1.6||Convert R Markdown documents into a variety of formats|
|r-rmtstat 0.3||Distributions, statistics and tests derived from random matrix theory|
|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.
|r-robust 0.4-18||Port of the S+ "Robust Library"|
|r-robustbase 0.92-7||Basic robust statistics|
|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.
|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
|r-roxygen2 6.0.1||In-source documentation system for R|
|r-rpart 4.1-11||Recursive partitioning and regression trees|
|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.
|r-rrcov 1.4-3||Scalable robust estimators with high breakdown Point|
|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.
|r-rsqlite 2.0||SQLite interface for R|
|r-rstudioapi 0.7||Safely access the RStudio API|
|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.
|r-rtsne 0.13||T-distributed stochastic neighbor embedding|
|r-runit 0.4.31||R unit test framework|
|r-rversions 1.0.3||Query R versions, including 'r-release' and 'r-oldrel'|
|r-s4vectors 0.14.3||S4 implementation of vectors and lists
The S4Vectors package defines the
|r-scales 0.5.0||Scale functions for visualization|
|r-segmented 0.5-2.2||Regression models with breakpoints estimation|
|r-sendmailr 1.2-1||Send email using R|
|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.
|r-seqinr 3.4-5||Biological sequences retrieval and analysis|
|r-seqlogo 1.42.0||Sequence logos for DNA sequence alignments|
|r-seqminer 6.0||Read nucleotide sequence data (VCF, BCF, and METAL formats)|
|r-seqpattern 1.8.0||Visualising oligonucleotide patterns and motif occurrences|
|r-servr 0.7||Simple HTTP server to serve static files or dynamic documents|
|r-seurat 184.108.40.206-1.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.
|r-sfsmisc 1.1-1||Utilities from "Seminar fuer Statistik" ETH Zurich|
|r-shape 1.4.3||Functions for plotting graphical shapes|
|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.
|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
|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.
|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
|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.
|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.
|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:
|r-sparql 1.16||SPARQL client for R|
|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.
|r-spatial 7.3-11||Functions for kriging and point pattern analysis|
|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.
|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.
|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.
|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.
|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.
|r-survival 2.41-3||Survival analysis|
|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.
|r-svglite 1.2.1||SVG graphics device
|r-synchronicity 220.127.116.11||Boost mutex functionality in R|
|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.
|r-tclust 1.3-1||Robust trimmed clustering|
|r-testthat 1.0.2||Unit testing for R|
|r-tibble 1.3.4||Simple data frames|
|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.
|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.
|r-timedate 3012.100||Chronological and calendar objects|
|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.
|r-trimcluster 0.1-2||Cluster analysis with trimming|
|r-tsne 0.1-3||t-Distributed Stochastic Neighbor Embedding for R|
|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
|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.
|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.
|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.
|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.
|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.
|r-vipor 0.4.5||Plot categorical data using noise and density estimates|
|r-viridis 0.4.0||Matplotlib default color map
This package is a port of the new http://matplotlib.org/ color maps (
|r-viridislite 0.2.0||Default color maps from matplotlib
This package is a port of the new
|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.
|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.
|r-whisker 0.3-2||Logicless mustache templating for R|
|r-withr 2.0.0||Run code with temporarily modified global state|
|r-xml 3.98-1.9||Tools for parsing and generating XML within R|
|r-xml2 1.1.1||Parse XML with R|
|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
|r-xtable 1.8-2||Export R tables to LaTeX or HTML|
|r-xvector 0.16.0||Representation and manpulation of external sequences|
|r-yaml 2.1.14||Methods to convert R data to YAML and back|
|r-zlibbioc 1.22.0||Provider for zlib-1.2.5 to R packages|
|r-zoo 1.8-0||S3 infrastructure for regular and irregular time series|
|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
|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.
|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, ...
|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.
|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.
|rage 0.2.1||Video and audio player based on EFL|
|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.
|raincat 18.104.22.168||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.
|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.
|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.
|randrproto 1.5.0||Xorg RandRProto protocol headers|
|rapicorn 16.0.0||Toolkit for rapid development of user interfaces|
|rapidjson 1.1.0||JSON parser/generator for C++ with both SAX/DOM style API|
|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.
|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.
|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.
|raul 0.8.0||Real-time audio utility library|
|raul 0.8.4-1.f8bf77d3c||Real-time audio utility library|
|raxml 8.2.10||Randomized Axelerated Maximum Likelihood phylogenetic trees
RAxML is a tool for phylogenetic analysis and post-analysis of large phylogenies.
|rc 1.7.4||Alternative implementation of the rc shell by Byron Rakitzis|
|rcas-web 0.0.4||Web interface for RNA-centric annotation system (RCAS)|
|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.
|rdesktop 1.8.3||Client for Windows Terminal Services|
|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.
|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:
The following service daemons are also provided:
X11-style (This is an X11-style, non-copyleft free software license. Check the URI for details. )
|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.
|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.
|re2 2017-08-01||Fast, safe, thread-friendly regular expression engine|
|re2c 0.16||Lexer generator for C/C++
|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.
|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.
|recode 22.214.171.124402||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.
|recordmydesktop 0.3.8.1||Desktop session video recorder|
|recordproto 1.14.2||Xorg RecordProto protocol headers|
|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.
|red-eclipse 1.5.8-2||Arena shooter derived from the Cube 2 engine|
|redis 4.0.1||Key-value cache and store|
|redland 1.0.17||RDF library|
|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.
|reducelcs 1.0-1.474f88d||Approximate Longest Commons Subsequence computation tool|
|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.
|renderproto 0.11.1||Xorg RenderProto protocol headers|
|rep-gtk 0.90.8.2||GTK+ binding for librep|
|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).
|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
|resourceproto 1.2.0||Xorg ResourceProto protocol headers|
|rest 0.8.0||RESTful web api query library|
|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.
|retux 1.3.5||Action platformer game|
|rev-plugins 0.7.1||LADSPA reverb plugin|
|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
|rhythmbox 3.4.1||Music player for GNOME|
|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.
|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.
|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.
|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.
|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.
|rkflashtool 0.0.0-1.094bd64||Tools for flashing Rockchip devices|
|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.
|rmath-standalone 3.4.2||Standalone R math library|
|rng-tools 5||Random number generator daemon|
|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.
|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
|roffit 0.11-1.e5228388e||Convert nroff files to HTML|
|rofi 1.4.1||Application launcher|
|rosegarden 17.04||Music composition and editing environment based around a MIDI sequencer|
|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.
|rpcbind 0.2.4||Server to convert RPC program numbers into universal addresses|
|rpm 126.96.36.199||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.
|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.
|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.
|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.
|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.
|rsound 1.1||Networked audio system|
|rss-bridge 2017-08-03||Generate Atom feeds for social networking websites|
|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.
|rtl-sdr 0.5.3||Software defined radio driver for Realtek RTL2832U|
|rtmidi 2.1.0||Cross-platform MIDI library for C++|
|rtorrent 0.9.6||BitTorrent client with ncurses interface|
|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.
|rubberband 1.8.1||Audio time-stretching and pitch-shifting library|
|ruby 2.3.5||Programming language interpreter|
|ruby 2.4.2||Programming language interpreter|
|ruby 2.2.8||Programming language interpreter|
|ruby 2.1.10||Programming language interpreter|
|ruby 1.8.7-p374||Programming language interpreter|
|ruby-activesupport 5.1.4||Ruby on Rails utility library|
|ruby-ae 1.8.2||Assertions library|
|ruby-afm 0.2.2||Read Adobe Font Metrics (afm) files|
|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
|ruby-arel 8.0.0||SQL AST manager for Ruby|
|ruby-ascii85 1.0.2||Encode and decode Ascii85 binary-to-text encoding|
|ruby-atoulme-antwrap 0.7.5||Ruby wrapper for the Ant build tool|
|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.
|ruby-bacon 1.2.0||Small RSpec clone|
|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
|ruby-bio-kseq 0.0.2||Ruby bindings for the kseq.h FASTA/Q parser|
|ruby-bio-logger 1.0.1||Log4r wrapper for Ruby|
|ruby-blankslate 3.1.3||Abstract base class with no predefined methods|
|ruby-brass 1.2.1||Basic foundational assertions framework|
|ruby-builder 3.2.3||Ruby library to create structured data|
|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.
|ruby-ci-reporter 2.0.0||Generate XML reports of runs test
|ruby-clap 1.0.0||Command line argument parsing for simple applications|
|ruby-code-statistics 0.2.13||Port of the rails 'rake stats' method|
|ruby-coderay 1.1.2||Ruby syntax highlighting library|
|ruby-concurrent 1.0.5||Concurrency tools for Ruby
|ruby-connection-pool 2.2.1||Generic connection pool for Ruby|
|ruby-crass 1.0.2||Pure Ruby CSS parser|
|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.
|ruby-cutest 1.2.2||Run tests in separate processes|
|ruby-daemons 1.2.4||Daemonize Ruby programs|
|ruby-debug-inspector 0.0.3||Ruby wrapper for the MRI 2.0 debug_inspector API|
|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.
|ruby-docile 1.1.5||Ruby EDSL helper library|
|ruby-domain-name 0.5.20170404||Domain name manipulation library
|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.
|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.
|ruby-fivemat 1.3.5||Each test file given its own line of dots|
|ruby-formatador 0.2.5||Ruby library to format text on stdout|
|ruby-gem-hadar 1.9.1||Library for the development of Ruby gems|
|ruby-gettext 3.1.7||GNU gettext-like program for Ruby|
|ruby-gherkin 4.1.3||Gherkin parser for Ruby|
|ruby-git 1.3.0||Ruby wrappers for Git|
|ruby-guard 2.13.0||Tool to handle events on file system modifications|
|ruby-hashery 2.1.2||Hash-like classes with extra features
The Hashery is a tight collection of
|ruby-highline 1.7.8||HighLine helps you build command-line interfaces|
|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.
|ruby-hoe-git 1.6.0||Hoe plugins for tighter Git integration|
|ruby-http-cookie 1.0.3||Handle HTTP Cookies based on RFC 6265|
|ruby-httpclient 2.8.3||Make HTTP requests with support for HTTPS, Cookies, authentication and more|
|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.
|ruby-instantiator 0.0.6||Instantiate an arbitrary Ruby class|
|ruby-introspection 0.0.4||Dynamic inspection of the method hierarchy on a Ruby object|
|ruby-json 2.1.0||JSON library for Ruby|
|ruby-json-pure 2.1.0||JSON implementation in pure Ruby|
|ruby-lemon 0.9.1||Test framework correlating code structure and test unit|
|ruby-libxml 3.0.0||Ruby bindings for GNOME Libxml2|
|ruby-listen 3.1.5||Listen to file modifications|
|ruby-locale 2.1.2||Ruby library providing basic localization APIs|
|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.
|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.
|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
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.
|ruby-metaclass 0.0.4||Ruby library adding metaclass method to all objects|
|ruby-method-source 0.9.0||Retrieve the source code for Ruby methods|
|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.
|ruby-mime-types-data 3.2016.0521||Registry for information about MIME media type definitions
|ruby-mini-portile 0.6.2||Ports system for Ruby developers|
|ruby-mini-portile 2.2.0||Ports system for Ruby developers|
|ruby-minitar 0.5.4-1.e25205ec||Ruby library and utility for handling tar archives|
|ruby-minitest 4.7.5||Small test suite library for Ruby|
|ruby-minitest 5.10.3||Small test suite library for Ruby|
|ruby-minitest-bacon 1.0.3||Bacon compatibility library for minitest|
|ruby-minitest-bonus-assertions 3.0||Bonus assertions for
Minitest bonus assertions provides extra MiniTest assertions. For instance, it provides
|ruby-minitest-focus 1.1.2||Allows a few specific tests to be focused on
|ruby-minitest-hooks 1.4.1||Hooks for the minitest framework
|ruby-minitest-moar 0.0.4||Extra features and changes to MiniTest|
|ruby-minitest-pretty-diff 0.1-1.11f32e93||Pretty-print hashes and arrays in MiniTest|
|ruby-minitest-rg 5.2.0||Coloured output for Minitest|
|ruby-minitest-sprint 1.1.0||Fast test suite runner for minitest|
|ruby-minitest-tu-shim 1.3.3||Adapter library between minitest and test/unit|
|ruby-mocha 1.1.0||Mocking and stubbing library for Ruby|
|ruby-multi-json 1.12.2||Common interface to multiple JSON libraries for Ruby|
|ruby-multipart-post 2.0.0||Multipart POST library for Ruby|
|ruby-nenv 0.3.0||Ruby interface for modifying the environment|
|ruby-net-http-digest-auth 1.4.1||RFC 2617 HTTP digest authentication library|
|ruby-net-http-persistent 3.0.0||Persistent HTTP connection manager|
|ruby-net-ssh 4.1.0||Ruby implementation of the SSH2 client protocol|
|ruby-netrc 0.11.0||Library to read and update netrc files|
|ruby-nokogiri 1.8.0||HTML, XML, SAX, and Reader parser for Ruby|
|ruby-nokogiri-diff 0.2.0-1.a38491e4||Calculate the differences between two XML/HTML documents|
|ruby-nokogumbo 1.4.7-1.fb51ff29||Ruby bindings to the Gumbo HTML5 parser|
|ruby-notiffany 0.1.1||Wrapper libray for notification libraries|
|ruby-options 2.3.2||Ruby library to parse options from *args cleanly|
|ruby-orderedhash 0.0.6||Ruby library providing an order-preserving hash|
|ruby-ox 2.6.0||Optimized XML library for Ruby|