Package Index


[Top]

Packages in the standard library

A B C D E F G H I J K L M N O P R S T U V W X Y Z

affyMethods for Affymetrix Oligonucleotide Arrays
affyioTools for parsing Affymetrix data files
airwayRangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
annotateAnnotation for microarrays
AnnotationDbiManipulation of SQLite-based annotations in Bioconductor
AnnotationFilterFacilities for Filtering Bioconductor Annotation Resources
AnnotationHubClient to access AnnotationHub resources
apeglmApproximate posterior estimation for GLM coefficients
askpassSafe Password Entry for R, Git, and SSH
assertthatEasy Pre and Post Assertions
backportsReimplementations of Functions Introduced Since R-3.0.0
baseThe R Base Package
base64encTools for base64 encoding
bbmleTools for General Maximum Likelihood Estimation
bdsmatrixRoutines for Block Diagonal Symmetric Matrices
beeswarmThe Bee Swarm Plot, an Alternative to Stripchart
BHBoost C++ Header Files
BiobaseBiobase: Base functions for Bioconductor
BiocFileCacheManage Files Across Sessions
BiocGenericsS4 generic functions used in Bioconductor
BiocManagerAccess the Bioconductor Project Package Repository
BiocParallelBioconductor facilities for parallel evaluation
BiocVersionSet the appropriate version of Bioconductor packages
biomaRtInterface to BioMart databases (i.e. Ensembl)
BiostringsEfficient manipulation of biological strings
bitClasses and Methods for Fast Memory-Efficient Boolean Selections
bit64A S3 Class for Vectors of 64bit Integers
bitopsBitwise Operations
blobA Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
broomConvert Statistical Objects into Tidy Tibbles
callrCall R from R
caToolsTools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
cellrangerTranslate Spreadsheet Cell Ranges to Rows and Columns
cliHelpers for Developing Command Line Interfaces
cliprRead and Write from the System Clipboard
codaOutput Analysis and Diagnostics for MCMC
colorspaceA Toolbox for Manipulating and Assessing Colors and Palettes
commonmarkHigh Performance CommonMark and Github Markdown Rendering in R
compilerThe R Compiler Package
configManage Environment Specific Configuration Values
crayonColored Terminal Output
curlA Modern and Flexible Web Client for R
data.tableExtension of `data.frame`
datasetsThe R Datasets Package
DBIR Database Interface
dbplyrA 'dplyr' Back End for Databases
DelayedArrayA unified framework for working transparently with on-disk and in-memory array-like datasets
descManipulate DESCRIPTION Files
DESeq2Differential gene expression analysis based on the negative binomial distribution
DEXSeqInference of differential exon usage in RNA-Seq
digestCreate Compact Hash Digests of R Objects
dplyrA Grammar of Data Manipulation
DRIMSeqDifferential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
edgeREmpirical Analysis of Digital Gene Expression Data in R
ellipsisTools for Working with ...
emdbookSupport Functions and Data for "Ecological Models and Data"
ensembldbUtilities to create and use Ensembl-based annotation databases
evaluateParsing and Evaluation Tools that Provide More Details than the Default
fansiANSI Control Sequence Aware String Functions
farverHigh Performance Colour Space Manipulation
fastmapFast Implementation of a Key-Value Store
fastmatchFast match() function
fgseaFast Gene Set Enrichment Analysis
forcatsTools for Working with Categorical Variables (Factors)
formatRFormat R Code Automatically
fsCross-Platform File System Operations Based on 'libuv'
futile.loggerA Logging Utility for R
futile.optionsFutile Options Management
genefiltergenefilter: methods for filtering genes from high-throughput experiments
geneplotterGraphics related functions for Bioconductor
genericsCommon S3 Generics not Provided by Base R Methods Related to Model Fitting
GenomeInfoDbUtilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbDataSpecies and taxonomy ID look up tables used by GenomeInfoDb
GenomicAlignmentsRepresentation and manipulation of short genomic alignments
GenomicFeaturesConveniently import and query gene models
GenomicRangesRepresentation and manipulation of genomic intervals
ggbeeswarmCategorical Scatter (Violin Point) Plots
ggplot2Create Elegant Data Visualisations Using the Grammar of Graphics
ggrepelAutomatically Position Non-Overlapping Text Labels with 'ggplot2'
ggvennDraw Venn Diagram by 'ggplot2'
glmpcaDimension Reduction of Non-Normally Distributed Data
glueInterpreted String Literals
gplotsVarious R Programming Tools for Plotting Data
graphicsThe R Graphics Package
grDevicesThe R Graphics Devices and Support for Colours and Fonts
gridThe Grid Graphics Package
gridExtraMiscellaneous Functions for "Grid" Graphics
gtableArrange 'Grobs' in Tables
gtoolsVarious R Programming Tools
havenImport and Export 'SPSS', 'Stata' and 'SAS' Files
hexbinHexagonal Binning Routines
highrSyntax Highlighting for R Source Code
hmsPretty Time of Day
htmltoolsTools for HTML
httpuvHTTP and WebSocket Server Library
httrTools for Working with URLs and HTTP
hwriterHTML Writer - Outputs R objects in HTML format
interactiveDisplayBaseBase package for enabling powerful shiny web displays of Bioconductor objects
IRangesFoundation of integer range manipulation in Bioconductor
isobandGenerate Isolines and Isobands from Regularly Spaced Elevation Grids
jsonliteA Robust, High Performance JSON Parser and Generator for R
kerasR Interface to 'Keras'
KernSmoothFunctions for Kernel Smoothing Supporting Wand & Jones (1995)
knitrA General-Purpose Package for Dynamic Report Generation in R
labelingAxis Labeling
lambda.rModeling Data with Functional Programming
laterUtilities for Scheduling Functions to Execute Later with Event Loops
latticeTrellis Graphics for R
lazyevalLazy (Non-Standard) Evaluation
lifecycleManage the Life Cycle of your Package Functions
limmaLinear Models for Microarray Data
locfitLocal Regression, Likelihood and Density Estimation
lubridateMake Dealing with Dates a Little Easier
magrittrA Forward-Pipe Operator for R
markdownRender Markdown with the C Library 'Sundown'
MASSSupport Functions and Datasets for Venables and Ripley's MASS
MatrixSparse and Dense Matrix Classes and Methods
matrixStatsFunctions that Apply to Rows and Columns of Matrices (and to Vectors)
memoiseMemoisation of Functions
methodsFormal Methods and Classes
mgcvMixed GAM Computation Vehicle with Automatic Smoothness Estimation
mimeMap Filenames to MIME Types
modelrModelling Functions that Work with the Pipe
msigdbrMSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
munsellUtilities for Using Munsell Colours
mvtnormMultivariate Normal and t Distributions
nlmeLinear and Nonlinear Mixed Effects Models
numDerivAccurate Numerical Derivatives
opensslToolkit for Encryption, Signatures and Certificates Based on OpenSSL
org.Hs.eg.dbGenome wide annotation for Human
parallelSupport for Parallel computation in R
pheatmapPretty Heatmaps
pillarColoured Formatting for Columns
pkgbuildFind Tools Needed to Build R Packages
pkgconfigPrivate Configuration for 'R' Packages
pkgloadSimulate Package Installation and Attach
plogrThe 'plog' C++ Logging Library
plyrTools for Splitting, Applying and Combining Data
praisePraise Users
preprocessCoreA collection of pre-processing functions
prettyunitsPretty, Human Readable Formatting of Quantities
processxExecute and Control System Processes
progressTerminal Progress Bars
promisesAbstractions for Promise-Based Asynchronous Programming
ProtGenericsS4 generic functions for Bioconductor proteomics infrastructure
psList, Query, Manipulate System Processes
purrrFunctional Programming Tools
R6Encapsulated Classes with Reference Semantics
rappdirsApplication Directories: Determine Where to Save Data, Caches, and Logs
RColorBrewerColorBrewer Palettes
RcppSeamless R and C++ Integration
RcppArmadillo'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
RcppEigen'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
RcppNumerical'Rcpp' Integration for Numerical Computing Libraries
RCurlGeneral Network (HTTP/FTP/...) Client Interface for R
readrRead Rectangular Text Data
readxlRead Excel Files
rematchMatch Regular Expressions with a Nicer 'API'
reprexPrepare Reproducible Example Code via the Clipboard
reshape2Flexibly Reshape Data: A Reboot of the Reshape Package
reticulateInterface to 'Python'
RhtslibHTSlib high-throughput sequencing library as an R package
rlangFunctions for Base Types and Core R and 'Tidyverse' Features
rmarkdownDynamic Documents for R
rprojrootFinding Files in Project Subdirectories
RsamtoolsBinary alignment (BAM), FASTA, variant call (BCF), and tabix file import
RSQLite'SQLite' Interface for R
rstudioapiSafely Access the RStudio API
rtracklayerR interface to genome annotation files and the UCSC genome browser
rvestEasily Harvest (Scrape) Web Pages
S4VectorsFoundation of vector-like and list-like containers in Bioconductor
scalesScale Functions for Visualization
selectrTranslate CSS Selectors to XPath Expressions
shinyWeb Application Framework for R
snowSimple Network of Workstations
sourcetoolsTools for Reading, Tokenizing and Parsing R Code
splinesRegression Spline Functions and Classes
stageRstageR: stage-wise analysis of high throughput gene expression data in R
statmodStatistical Modeling
statsThe R Stats Package
stats4Statistical Functions using S4 Classes
stringiCharacter String Processing Facilities
stringrSimple, Consistent Wrappers for Common String Operations
SummarizedExperimentSummarizedExperiment container
survivalSurvival Analysis
sysPowerful and Reliable Tools for Running System Commands in R
tcltkTcl/Tk Interface
tensorflowR Interface to 'TensorFlow'
testthatUnit Testing for R
tfrunsTraining Run Tools for 'TensorFlow'
tibbleSimple Data Frames
tidyrTidy Messy Data
tidyselectSelect from a Set of Strings
tidyverseEasily Install and Load the 'Tidyverse'
tinytexHelper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
toolsTools for Package Development
tximetaTranscript Quantification Import with Automatic Metadata
tximportImport and summarize transcript-level estimates for transcript- and gene-level analysis
utf8Unicode Text Processing
utilsThe R Utils Package
vctrsVector Helpers
viporPlot Categorical Data Using Quasirandom Noise and Density Estimates
viridisLiteDefault Color Maps from 'matplotlib' (Lite Version)
vsnVariance stabilization and calibration for microarray data
whisker{{mustache}} for R, Logicless Templating
withrRun Code 'With' Temporarily Modified Global State
xfunMiscellaneous Functions by 'Yihui Xie'
XMLTools for Parsing and Generating XML Within R and S-Plus
xml2Parse XML
xtableExport Tables to LaTeX or HTML
XVectorFoundation of external vector representation and manipulation in Bioconductor
yamlMethods to Convert R Data to YAML and Back
zeallotMultiple, Unpacking, and Destructuring Assignment
zlibbiocAn R packaged zlib-1.2.5