Package Index

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

affy Methods for Affymetrix Oligonucleotide Arrays

affyio Tools for parsing Affymetrix data files

airway RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014

annotate Annotation for microarrays

AnnotationDbi Manipulation of SQLite-based annotations in Bioconductor

AnnotationFilter Facilities for Filtering Bioconductor Annotation Resources

AnnotationHub Client to access AnnotationHub resources

apeglm Approximate posterior estimation for GLM coefficients

askpass Safe Password Entry for R, Git, and SSH

assertthat Easy Pre and Post Assertions

backports Reimplementations of Functions Introduced Since R-3.0.0

base The R Base Package

base64enc Tools for base64 encoding

bbmle Tools for General Maximum Likelihood Estimation

bdsmatrix Routines for Block Diagonal Symmetric Matrices

beeswarm The Bee Swarm Plot, an Alternative to Stripchart

BH Boost C++ Header Files

Biobase Biobase: Base functions for Bioconductor

BiocFileCache Manage Files Across Sessions

BiocGenerics S4 generic functions used in Bioconductor

BiocManager Access the Bioconductor Project Package Repository

BiocParallel Bioconductor facilities for parallel evaluation

BiocVersion Set the appropriate version of Bioconductor packages

biomaRt Interface to BioMart databases (i.e. Ensembl)

Biostrings Efficient manipulation of biological strings

bit Classes and Methods for Fast Memory-Efficient Boolean Selections

bit64 A S3 Class for Vectors of 64bit Integers

bitops Bitwise Operations

blob A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')

broom Convert Statistical Objects into Tidy Tibbles

callr Call R from R

caTools Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc

cellranger Translate Spreadsheet Cell Ranges to Rows and Columns

cli Helpers for Developing Command Line Interfaces

clipr Read and Write from the System Clipboard

coda Output Analysis and Diagnostics for MCMC

colorspace A Toolbox for Manipulating and Assessing Colors and Palettes

commonmark High Performance CommonMark and Github Markdown Rendering in R

compiler The R Compiler Package

config Manage Environment Specific Configuration Values

crayon Colored Terminal Output

curl A Modern and Flexible Web Client for R

data.table Extension of `data.frame`

datasets The R Datasets Package

DBI R Database Interface

dbplyr A 'dplyr' Back End for Databases

DelayedArray A unified framework for working transparently with on-disk and in-memory array-like datasets

desc Manipulate DESCRIPTION Files

DESeq2 Differential gene expression analysis based on the negative binomial distribution

DEXSeq Inference of differential exon usage in RNA-Seq

digest Create Compact Hash Digests of R Objects

dplyr A Grammar of Data Manipulation

DRIMSeq Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

edgeR Empirical Analysis of Digital Gene Expression Data in R

ellipsis Tools for Working with ...

emdbook Support Functions and Data for "Ecological Models and Data"

ensembldb Utilities to create and use Ensembl-based annotation databases

evaluate Parsing and Evaluation Tools that Provide More Details than the Default

fansi ANSI Control Sequence Aware String Functions

farver High Performance Colour Space Manipulation

fastmap Fast Implementation of a Key-Value Store

fastmatch Fast match() function

fgsea Fast Gene Set Enrichment Analysis

forcats Tools for Working with Categorical Variables (Factors)

formatR Format R Code Automatically

fs Cross-Platform File System Operations Based on 'libuv'

futile.logger A Logging Utility for R

futile.options Futile Options Management

genefilter genefilter: methods for filtering genes from high-throughput experiments

geneplotter Graphics related functions for Bioconductor

generics Common S3 Generics not Provided by Base R Methods Related to Model Fitting

GenomeInfoDb Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

GenomeInfoDbData Species and taxonomy ID look up tables used by GenomeInfoDb

GenomicAlignments Representation and manipulation of short genomic alignments

GenomicFeatures Conveniently import and query gene models

GenomicRanges Representation and manipulation of genomic intervals

ggbeeswarm Categorical Scatter (Violin Point) Plots

ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics

ggrepel Automatically Position Non-Overlapping Text Labels with 'ggplot2'

ggvenn Draw Venn Diagram by 'ggplot2'

glmpca Dimension Reduction of Non-Normally Distributed Data

glue Interpreted String Literals

gplots Various R Programming Tools for Plotting Data

graphics The R Graphics Package

grDevices The R Graphics Devices and Support for Colours and Fonts

grid The Grid Graphics Package

gridExtra Miscellaneous Functions for "Grid" Graphics

gtable Arrange 'Grobs' in Tables

gtools Various R Programming Tools

haven Import and Export 'SPSS', 'Stata' and 'SAS' Files

hexbin Hexagonal Binning Routines

highr Syntax Highlighting for R Source Code

hms Pretty Time of Day

htmltools Tools for HTML

httpuv HTTP and WebSocket Server Library

httr Tools for Working with URLs and HTTP

hwriter HTML Writer - Outputs R objects in HTML format

interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects

IRanges Foundation of integer range manipulation in Bioconductor

isoband Generate Isolines and Isobands from Regularly Spaced Elevation Grids

jsonlite A Robust, High Performance JSON Parser and Generator for R

keras R Interface to 'Keras'

KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995)

knitr A General-Purpose Package for Dynamic Report Generation in R

labeling Axis Labeling

lambda.r Modeling Data with Functional Programming

later Utilities for Scheduling Functions to Execute Later with Event Loops

lattice Trellis Graphics for R

lazyeval Lazy (Non-Standard) Evaluation

lifecycle Manage the Life Cycle of your Package Functions

limma Linear Models for Microarray Data

locfit Local Regression, Likelihood and Density Estimation

lubridate Make Dealing with Dates a Little Easier

magrittr A Forward-Pipe Operator for R

markdown Render Markdown with the C Library 'Sundown'

MASS Support Functions and Datasets for Venables and Ripley's MASS

Matrix Sparse and Dense Matrix Classes and Methods

matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors)

memoise Memoisation of Functions

methods Formal Methods and Classes

mgcv Mixed GAM Computation Vehicle with Automatic Smoothness Estimation

mime Map Filenames to MIME Types

modelr Modelling Functions that Work with the Pipe

msigdbr MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format

munsell Utilities for Using Munsell Colours

mvtnorm Multivariate Normal and t Distributions

nlme Linear and Nonlinear Mixed Effects Models

numDeriv Accurate Numerical Derivatives

openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL

org.Hs.eg.db Genome wide annotation for Human

parallel Support for Parallel computation in R

pheatmap Pretty Heatmaps

pillar Coloured Formatting for Columns

pkgbuild Find Tools Needed to Build R Packages

pkgconfig Private Configuration for 'R' Packages

pkgload Simulate Package Installation and Attach

plogr The 'plog' C++ Logging Library

plyr Tools for Splitting, Applying and Combining Data

praise Praise Users

preprocessCore A collection of pre-processing functions

prettyunits Pretty, Human Readable Formatting of Quantities

processx Execute and Control System Processes

progress Terminal Progress Bars

promises Abstractions for Promise-Based Asynchronous Programming

ProtGenerics S4 generic functions for Bioconductor proteomics infrastructure

ps List, Query, Manipulate System Processes

purrr Functional Programming Tools

R6 Encapsulated Classes with Reference Semantics

rappdirs Application Directories: Determine Where to Save Data, Caches, and Logs

RColorBrewer ColorBrewer Palettes

Rcpp Seamless 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

RCurl General Network (HTTP/FTP/...) Client Interface for R

readr Read Rectangular Text Data

readxl Read Excel Files

rematch Match Regular Expressions with a Nicer 'API'

reprex Prepare Reproducible Example Code via the Clipboard

reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package

reticulate Interface to 'Python'

Rhtslib HTSlib high-throughput sequencing library as an R package

rlang Functions for Base Types and Core R and 'Tidyverse' Features

rmarkdown Dynamic Documents for R

rprojroot Finding Files in Project Subdirectories

Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

RSQLite 'SQLite' Interface for R

rstudioapi Safely Access the RStudio API

rtracklayer R interface to genome annotation files and the UCSC genome browser

rvest Easily Harvest (Scrape) Web Pages

S4Vectors Foundation of vector-like and list-like containers in Bioconductor

scales Scale Functions for Visualization

selectr Translate CSS Selectors to XPath Expressions

shiny Web Application Framework for R

snow Simple Network of Workstations

sourcetools Tools for Reading, Tokenizing and Parsing R Code

splines Regression Spline Functions and Classes

stageR stageR: stage-wise analysis of high throughput gene expression data in R

statmod Statistical Modeling

stats The R Stats Package

stats4 Statistical Functions using S4 Classes

stringi Character String Processing Facilities

stringr Simple, Consistent Wrappers for Common String Operations

SummarizedExperiment SummarizedExperiment container

survival Survival Analysis

sys Powerful and Reliable Tools for Running System Commands in R

tcltk Tcl/Tk Interface

tensorflow R Interface to 'TensorFlow'

testthat Unit Testing for R

tfruns Training Run Tools for 'TensorFlow'

tibble Simple Data Frames

tidyr Tidy Messy Data

tidyselect Select from a Set of Strings

tidyverse Easily Install and Load the 'Tidyverse'

tinytex Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents

tools Tools for Package Development

tximeta Transcript Quantification Import with Automatic Metadata

tximport Import and summarize transcript-level estimates for transcript- and gene-level analysis

utf8 Unicode Text Processing

utils The R Utils Package

vctrs Vector Helpers

vipor Plot Categorical Data Using Quasirandom Noise and Density Estimates

viridisLite Default Color Maps from 'matplotlib' (Lite Version)

vsn Variance stabilization and calibration for microarray data

whisker {{mustache}} for R, Logicless Templating

withr Run Code 'With' Temporarily Modified Global State

xfun Miscellaneous Functions by 'Yihui Xie'

XML Tools for Parsing and Generating XML Within R and S-Plus

xml2 Parse XML

xtable Export Tables to LaTeX or HTML

XVector Foundation of external vector representation and manipulation in Bioconductor

yaml Methods to Convert R Data to YAML and Back

zeallot Multiple, Unpacking, and Destructuring Assignment

zlibbioc An R packaged zlib-1.2.5


affy	Methods for Affymetrix Oligonucleotide Arrays
affyio	Tools for parsing Affymetrix data files
airway	RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
annotate	Annotation for microarrays
AnnotationDbi	Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter	Facilities for Filtering Bioconductor Annotation Resources
AnnotationHub	Client to access AnnotationHub resources
apeglm	Approximate posterior estimation for GLM coefficients
askpass	Safe Password Entry for R, Git, and SSH
assertthat	Easy Pre and Post Assertions

backports	Reimplementations of Functions Introduced Since R-3.0.0
base	The R Base Package
base64enc	Tools for base64 encoding
bbmle	Tools for General Maximum Likelihood Estimation
bdsmatrix	Routines for Block Diagonal Symmetric Matrices
beeswarm	The Bee Swarm Plot, an Alternative to Stripchart
BH	Boost C++ Header Files
Biobase	Biobase: Base functions for Bioconductor
BiocFileCache	Manage Files Across Sessions
BiocGenerics	S4 generic functions used in Bioconductor
BiocManager	Access the Bioconductor Project Package Repository
BiocParallel	Bioconductor facilities for parallel evaluation
BiocVersion	Set the appropriate version of Bioconductor packages
biomaRt	Interface to BioMart databases (i.e. Ensembl)
Biostrings	Efficient manipulation of biological strings
bit	Classes and Methods for Fast Memory-Efficient Boolean Selections
bit64	A S3 Class for Vectors of 64bit Integers
bitops	Bitwise Operations
blob	A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
broom	Convert Statistical Objects into Tidy Tibbles

callr	Call R from R
caTools	Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc
cellranger	Translate Spreadsheet Cell Ranges to Rows and Columns
cli	Helpers for Developing Command Line Interfaces
clipr	Read and Write from the System Clipboard
coda	Output Analysis and Diagnostics for MCMC
colorspace	A Toolbox for Manipulating and Assessing Colors and Palettes
commonmark	High Performance CommonMark and Github Markdown Rendering in R
compiler	The R Compiler Package
config	Manage Environment Specific Configuration Values
crayon	Colored Terminal Output
curl	A Modern and Flexible Web Client for R

data.table	Extension of `data.frame`
datasets	The R Datasets Package
DBI	R Database Interface
dbplyr	A 'dplyr' Back End for Databases
DelayedArray	A unified framework for working transparently with on-disk and in-memory array-like datasets
desc	Manipulate DESCRIPTION Files
DESeq2	Differential gene expression analysis based on the negative binomial distribution
DEXSeq	Inference of differential exon usage in RNA-Seq
digest	Create Compact Hash Digests of R Objects
dplyr	A Grammar of Data Manipulation
DRIMSeq	Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

edgeR	Empirical Analysis of Digital Gene Expression Data in R
ellipsis	Tools for Working with ...
emdbook	Support Functions and Data for "Ecological Models and Data"
ensembldb	Utilities to create and use Ensembl-based annotation databases
evaluate	Parsing and Evaluation Tools that Provide More Details than the Default

fansi	ANSI Control Sequence Aware String Functions
farver	High Performance Colour Space Manipulation
fastmap	Fast Implementation of a Key-Value Store
fastmatch	Fast match() function
fgsea	Fast Gene Set Enrichment Analysis
forcats	Tools for Working with Categorical Variables (Factors)
formatR	Format R Code Automatically
fs	Cross-Platform File System Operations Based on 'libuv'
futile.logger	A Logging Utility for R
futile.options	Futile Options Management

genefilter	genefilter: methods for filtering genes from high-throughput experiments
geneplotter	Graphics related functions for Bioconductor
generics	Common S3 Generics not Provided by Base R Methods Related to Model Fitting
GenomeInfoDb	Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData	Species and taxonomy ID look up tables used by GenomeInfoDb
GenomicAlignments	Representation and manipulation of short genomic alignments
GenomicFeatures	Conveniently import and query gene models
GenomicRanges	Representation and manipulation of genomic intervals
ggbeeswarm	Categorical Scatter (Violin Point) Plots
ggplot2	Create Elegant Data Visualisations Using the Grammar of Graphics
ggrepel	Automatically Position Non-Overlapping Text Labels with 'ggplot2'
ggvenn	Draw Venn Diagram by 'ggplot2'
glmpca	Dimension Reduction of Non-Normally Distributed Data
glue	Interpreted String Literals
gplots	Various R Programming Tools for Plotting Data
graphics	The R Graphics Package
grDevices	The R Graphics Devices and Support for Colours and Fonts
grid	The Grid Graphics Package
gridExtra	Miscellaneous Functions for "Grid" Graphics
gtable	Arrange 'Grobs' in Tables
gtools	Various R Programming Tools

haven	Import and Export 'SPSS', 'Stata' and 'SAS' Files
hexbin	Hexagonal Binning Routines
highr	Syntax Highlighting for R Source Code
hms	Pretty Time of Day
htmltools	Tools for HTML
httpuv	HTTP and WebSocket Server Library
httr	Tools for Working with URLs and HTTP
hwriter	HTML Writer - Outputs R objects in HTML format

interactiveDisplayBase	Base package for enabling powerful shiny web displays of Bioconductor objects
IRanges	Foundation of integer range manipulation in Bioconductor
isoband	Generate Isolines and Isobands from Regularly Spaced Elevation Grids

jsonlite	A Robust, High Performance JSON Parser and Generator for R

keras	R Interface to 'Keras'
KernSmooth	Functions for Kernel Smoothing Supporting Wand & Jones (1995)
knitr	A General-Purpose Package for Dynamic Report Generation in R

labeling	Axis Labeling
lambda.r	Modeling Data with Functional Programming
later	Utilities for Scheduling Functions to Execute Later with Event Loops
lattice	Trellis Graphics for R
lazyeval	Lazy (Non-Standard) Evaluation
lifecycle	Manage the Life Cycle of your Package Functions
limma	Linear Models for Microarray Data
locfit	Local Regression, Likelihood and Density Estimation
lubridate	Make Dealing with Dates a Little Easier

magrittr	A Forward-Pipe Operator for R
markdown	Render Markdown with the C Library 'Sundown'
MASS	Support Functions and Datasets for Venables and Ripley's MASS
Matrix	Sparse and Dense Matrix Classes and Methods
matrixStats	Functions that Apply to Rows and Columns of Matrices (and to Vectors)
memoise	Memoisation of Functions
methods	Formal Methods and Classes
mgcv	Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
mime	Map Filenames to MIME Types
modelr	Modelling Functions that Work with the Pipe
msigdbr	MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
munsell	Utilities for Using Munsell Colours
mvtnorm	Multivariate Normal and t Distributions

nlme	Linear and Nonlinear Mixed Effects Models
numDeriv	Accurate Numerical Derivatives

openssl	Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
org.Hs.eg.db	Genome wide annotation for Human

parallel	Support for Parallel computation in R
pheatmap	Pretty Heatmaps
pillar	Coloured Formatting for Columns
pkgbuild	Find Tools Needed to Build R Packages
pkgconfig	Private Configuration for 'R' Packages
pkgload	Simulate Package Installation and Attach
plogr	The 'plog' C++ Logging Library
plyr	Tools for Splitting, Applying and Combining Data
praise	Praise Users
preprocessCore	A collection of pre-processing functions
prettyunits	Pretty, Human Readable Formatting of Quantities
processx	Execute and Control System Processes
progress	Terminal Progress Bars
promises	Abstractions for Promise-Based Asynchronous Programming
ProtGenerics	S4 generic functions for Bioconductor proteomics infrastructure
ps	List, Query, Manipulate System Processes
purrr	Functional Programming Tools

R6	Encapsulated Classes with Reference Semantics
rappdirs	Application Directories: Determine Where to Save Data, Caches, and Logs
RColorBrewer	ColorBrewer Palettes
Rcpp	Seamless 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
RCurl	General Network (HTTP/FTP/...) Client Interface for R
readr	Read Rectangular Text Data
readxl	Read Excel Files
rematch	Match Regular Expressions with a Nicer 'API'
reprex	Prepare Reproducible Example Code via the Clipboard
reshape2	Flexibly Reshape Data: A Reboot of the Reshape Package
reticulate	Interface to 'Python'
Rhtslib	HTSlib high-throughput sequencing library as an R package
rlang	Functions for Base Types and Core R and 'Tidyverse' Features
rmarkdown	Dynamic Documents for R
rprojroot	Finding Files in Project Subdirectories
Rsamtools	Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
RSQLite	'SQLite' Interface for R
rstudioapi	Safely Access the RStudio API
rtracklayer	R interface to genome annotation files and the UCSC genome browser
rvest	Easily Harvest (Scrape) Web Pages

S4Vectors	Foundation of vector-like and list-like containers in Bioconductor
scales	Scale Functions for Visualization
selectr	Translate CSS Selectors to XPath Expressions
shiny	Web Application Framework for R
snow	Simple Network of Workstations
sourcetools	Tools for Reading, Tokenizing and Parsing R Code
splines	Regression Spline Functions and Classes
stageR	stageR: stage-wise analysis of high throughput gene expression data in R
statmod	Statistical Modeling
stats	The R Stats Package
stats4	Statistical Functions using S4 Classes
stringi	Character String Processing Facilities
stringr	Simple, Consistent Wrappers for Common String Operations
SummarizedExperiment	SummarizedExperiment container
survival	Survival Analysis
sys	Powerful and Reliable Tools for Running System Commands in R

tcltk	Tcl/Tk Interface
tensorflow	R Interface to 'TensorFlow'
testthat	Unit Testing for R
tfruns	Training Run Tools for 'TensorFlow'
tibble	Simple Data Frames
tidyr	Tidy Messy Data
tidyselect	Select from a Set of Strings
tidyverse	Easily Install and Load the 'Tidyverse'
tinytex	Helper Functions to Install and Maintain TeX Live, and Compile LaTeX Documents
tools	Tools for Package Development
tximeta	Transcript Quantification Import with Automatic Metadata
tximport	Import and summarize transcript-level estimates for transcript- and gene-level analysis

utf8	Unicode Text Processing
utils	The R Utils Package

vctrs	Vector Helpers
vipor	Plot Categorical Data Using Quasirandom Noise and Density Estimates
viridisLite	Default Color Maps from 'matplotlib' (Lite Version)
vsn	Variance stabilization and calibration for microarray data

whisker	{{mustache}} for R, Logicless Templating
withr	Run Code 'With' Temporarily Modified Global State

xfun	Miscellaneous Functions by 'Yihui Xie'
XML	Tools for Parsing and Generating XML Within R and S-Plus
xml2	Parse XML
xtable	Export Tables to LaTeX or HTML
XVector	Foundation of external vector representation and manipulation in Bioconductor

yaml	Methods to Convert R Data to YAML and Back

zeallot	Multiple, Unpacking, and Destructuring Assignment
zlibbioc	An R packaged zlib-1.2.5