Packages — R (Page 1 of 9)

r 3.5.0 — Environment for statistical computing and graphics

This is a GNU package.

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

r-abbyyr 0.5.4 — Access to Abbyy Optical Character Recognition (OCR) API

This package provides tools to get text from images of text using Abbyy Cloud Optical Character Recognition (OCR) API. With abbyyyR, one can easily OCR images, barcodes, forms, documents with machine readable zones, e.g. passports and get the results in a variety of formats including plain text and XML. To learn more about the Abbyy OCR API, see http://ocrsdk.com/.

r-abc 2.1 — Tools for Approximate Bayesian Computation (ABC)

This package implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit. Cross-validation tools are also available for measuring the accuracy of ABC estimates, and to calculate the misclassification probabilities of different models.

r-abc-data 1.0 — Data for Approximate Bayesian Computation (ABC) package

This package contains data which are used by functions of the abc package which implements several Approximate Bayesian Computation (ABC) algorithms for performing parameter estimation, model selection, and goodness-of-fit.

r-abind 1.4-5 — Combine multidimensional arrays

This package provides tools to combine multidimensional arrays into a single array. This is a generalization of cbind and rbind. It works with vectors, matrices, and higher-dimensional arrays. It also provides the functions adrop, asub, and afill for manipulating, extracting and replacing data in arrays.

r-acepack 1.4.1 — Functions for regression transformations

This package provides ACE and AVAS methods for choosing 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 1.7-11 — Multivariate data analysis and graphical display

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

r-affy 1.58.0 — Methods for affymetrix oligonucleotide arrays

This package contains functions for exploratory oligonucleotide array analysis.

r-affyio 1.50.0 — Tools for parsing Affymetrix data files

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

r-algdesign 1.1-7.3 — Algorithmic experimental design

This package provides tools to calculate exact and approximate theory experimental designs for D, A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.

r-amap 0.8-16 — Another multidimensional analysis package

This package provides tools for clustering and principal component analysis (with robust methods, and parallelized functions).

r-analytics 2.0 — Collection of data analysis tools

This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.

r-annotate 1.58.0 — Annotation for microarrays

This package provides R environments for the annotation of microarrays.

r-annotationdbi 1.42.1 — Annotation database interface

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

r-annotationfilter 1.4.0 — Facilities for filtering Bioconductor annotation resources

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

r-annotationforge 1.22.0 — Code for building annotation database packages

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

r-annotationhub 2.12.0 — Client to access AnnotationHub resources

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

r-ape 5.1 — 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-argparse 1.1.1 — Command line optional and positional argument parser

This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.

r-argparser 0.4 — Command-line argument parser

This package provides a cross-platform command-line argument parser written purely in R with no external dependencies. It is useful with the Rscript front-end and facilitates turning an R script into an executable script.

r-aroma-light 3.10.0 — 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-arules 1.6-1 — Mining association rules and frequent itemsets

This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat.

r-assertthat 0.2.0 — Easy pre and post assertions

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

r-auc 0.3.0 — Compute the area under the curve of selected measures

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

r-backports 1.1.2 — Reimplementations of functions introduced since R 3.0.0

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

r-bamsignals 1.12.1 — Extract read count signals from bam files

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

r-base64 2.0 — Base64 encoder and decoder

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

r-base64enc 0.1-3 — Tools for Base64 encoding

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

r-batchjobs 1.7 — Batch computing with R

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

r-bayseq 2.14.0 — Bayesian analysis of differential expression patterns in count data

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

r-bbmisc 1.11 — Miscellaneous functions for R package development

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

r-bbmle 1.0.20 — Tools for General Maximum Likelihood Estimation

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

r-beachmat 1.2.1 — Compiling Bioconductor to handle each matrix type

This package provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

r-beeswarm 0.2.3 — Implementation of bee swarm plots

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

r-bh 1.66.0-1 — R package providing subset of Boost headers

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

r-biased-urn 1.07 — Biased urn model distributions

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

r-biasedurn 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-bibtex 0.4.2 — Bibtex parser

This package provides a utility for R to parse a bibtex file.

r-bigmemory 4.5.33 — Manage large matrices with shared memory or memory-mapped files

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

r-bigmemory-sri 0.1.3 — Shared resource interface for the bigmemory package

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

r-bindr 0.1.1 — Parametrized active bindings

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

r-bindrcpp 0.2.2 — Rcpp interface to active bindings

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

r-biobase 2.40.0 — Base functions for Bioconductor

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

r-bioccheck 1.16.0 — Executes Bioconductor-specific package checks

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

r-biocgenerics 0.26.0 — S4 generic functions for Bioconductor

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

r-biocinstaller 1.30.0 — Install Bioconductor packages

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

r-biocparallel 1.14.1 — Bioconductor facilities for parallel evaluation

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

r-biocstyle 2.8.2 — Bioconductor formatting styles

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

r-biocviews 1.48.2 — Bioconductor package categorization helper

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

r-biomart 2.36.1 — 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 2.48.0 — String objects and algorithms for biological sequences

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

r-biovizbase 1.28.0 — Basic graphic utilities for visualization of genomic data

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

r-bit 1.1-14 — Class for vectors of 1-bit booleans

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

r-bit64 0.9-7 — S3 class for vectors of 64 bit integers

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

r-bitops 1.0-6 — Bitwise operations

This package provides functions for bitwise operations on integer vectors.

r-blob 1.1.1 — 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 0.7 — Authoring books and technical documents with R markdown

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

r-boot 1.3-20 — Bootstrap functions for R

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

r-brew 1.0-6 — Templating framework for report generation

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

r-broom 0.4.5 — Convert statistical analysis objects into tidy data frames

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

r-bsgenome 1.48.0 — Infrastructure for Biostrings-based genome data packages

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

r-bsgenome-celegans-ucsc-ce10 1.4.0 — Full genome sequences for Worm

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

r-bsgenome-celegans-ucsc-ce6 1.4.0 — Full genome sequences for Worm

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

r-bsgenome-dmelanogaster-ucsc-dm3 1.4.0 — Full genome sequences for Fly

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

r-bsgenome-dmelanogaster-ucsc-dm3-masked 1.3.99 — Full masked genome sequences for Fly

This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-bsgenome-dmelanogaster-ucsc-dm6 1.4.1 — Full genome sequences for Fly

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6) 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-hsapiens-ucsc-hg19-masked 1.3.99 — Full masked genome sequences for Homo sapiens

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

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-bsgenome-mmusculus-ucsc-mm9-masked 1.3.99 — Full masked genome sequences for Mouse

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-cairo 1.5-9 — R graphics device using Cairo graphics library

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

r-calibrate 1.7.2 — Calibration of scatterplot and biplot axes

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

r-callr 2.0.4 — Call R from R

It is sometimes useful to perform a computation in a separate R process, without affecting the current R process at all. This packages does exactly that.

r-car 3.0-0 — Companion to applied regression

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

r-cardata 3.0-1 — Data Sets for the book Companion to Applied Regression

This package provides datasets to accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage.

r-caret 6.0-80 — Classification and regression training

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

r-catdap 1.3.4 — Tools for categorical data analysis

This package provides functions for analyzing multivariate data. Dependencies of the distribution of the specified variable (response variable) to other variables (explanatory variables) are derived and evaluated by the Akaike Information Criterion (AIC).

r-category 2.46.0 — Category analysis

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

r-catools 1.17.1 — Various tools including functions for moving window statistics

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

r-catterplots 0-2.40063ec57 — Scatter plots with cat shaped points

Did you ever wish you could make scatter plots with cat shaped points? Now you can!

r-cellranger 1.1.0 — Translate spreadsheet cell ranges to rows and columns

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

r-centipede 1.2 — Predict transcription factor binding sites

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

r-cgdsr 1.2.10 — R-based API for accessing the MSKCC Cancer Genomics Data Server

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

r-cghbase 1.40.0 — Base functions and classes for arrayCGH data analysis

This package contains functions and classes that are needed by the arrayCGH packages.

r-cghcall 2.42.0 — Base functions and classes for arrayCGH data analysis

This package contains functions and classes that are needed by arrayCGH packages.

r-checkmate 1.8.5 — Fast and versatile argument checks

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

r-chipcomp 1.10.0 — Quantitative comparison of multiple ChIP-seq datasets

ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets.

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-chippeakanno 3.14.0 — Peaks annotation from ChIP-seq and ChIP-chip experiments

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).

r-chipseq 1.30.0 — Package for analyzing ChIPseq data

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

r-chron 2.3-52 — Chronological R objects which can handle dates and times

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

r-circlize 0.4.4 — Circular visualization

Circular layout is an efficient way to visualise huge amounts of information. This package provides an implementation of circular layout generation in R as well as an enhancement of available software. Its flexibility 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 multi-dimensional data.

r-class 7.3-14 — R functions for classification

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

r-cli 1.0.0 — Helpers for developing command line interfaces

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

r-cluster 2.0.7-1 — Methods for cluster analysis

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

r-coda 0.19-1 — This is a package for Output Analysis and Diagnostics for MCMC

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