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R Packagesยง

We provide a collection of installed R packages for each release of R, as a bundle module. This page lists the packages for the current recommended R bundle.

This can be loaded using:

module load r/recommended

The version of R provided with this bundle is currently R version 3.6.0 (2019-04-26).

The following list was last updated at: 15:32:24 (+0000) on 02 Feb 2021.

Module Version Description
AnnotationForge 1.26.0 Tools for building SQLite-based annotation data packages
BiocManager 1.30.4 Access the Bioconductor Project Package Repository
BiocVersion 3.9.0 Set the appropriate version of Bioconductor packages
Deriv 3.8.5 Symbolic Differentiation
dgo 0.2.15 Dynamic Estimation of Group-Level Opinion
dgodata 0.0.2 Data for the 'dgo' Package
digest 0.6.21 Create Compact Hash Digests of R Objects
GO.db 3.8.2 A set of annotation maps describing the entire Gene Ontology
hgu95av2.db 3.2.3 Affymetrix Human Genome U95 Set annotation data (chip hgu95av2)
HKprocess 0.0-2 Hurst-Kolmogorov Process
hugene10stprobeset.db 8.7.0 Affymetrix hugene10 annotation data (chip hugene10stprobeset)
hugene10sttranscriptcluster.db 8.7.0 Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)
Illumina450ProbeVariants.db 1.20.0 Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes
IlluminaHumanMethylation450kmanifest 0.4.0 Annotation for Illumina's 450k methylation arrays
illuminaHumanv4.db 1.26.0 Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)
INLA 19.09.03 Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
KEGG.db 3.2.3 A set of annotation maps for KEGG
MCMCpack 1.4-4 Markov Chain Monte Carlo (MCMC) Package
missMethyl 1.18.0 Analysing Illumina HumanMethylation BeadChip Data
org.Hs.eg.db 3.8.2 Genome wide annotation for Human
orthopolynom 1.0-5 Collection of functions for orthogonal and orthonormal polynomials
polynom 1.4-0 A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations
quanteda.corpora 0.87 A collection of corpora for quanteda
RcppZiggurat 0.1.5 'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations
Rfast 1.9.9 A Collection of Efficient and Extremely Fast R Functions
sf 0.7-7 Simple Features for R
splancs 2.01-40 Spatial and Space-Time Point Pattern Analysis
abc 2.1 Tools for Approximate Bayesian Computation (ABC)
abc.data 1.0 Data Only: Tools for Approximate Bayesian Computation (ABC)
abind 1.4-5 Combine Multidimensional Arrays
acepack 1.4.1 ACE and AVAS for Selecting Multiple Regression Transformations
adapt 1.0-4 adapt -- multidimensional numerical integration
ade4 1.7-13 Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences
adegenet 2.1.1 Exploratory Analysis of Genetic and Genomic Data
ADGofTest 0.3 Anderson-Darling GoF test
affxparser 1.56.0 Affymetrix File Parsing SDK
affy 1.62.0 Methods for Affymetrix Oligonucleotide Arrays
affydata 1.32.0 Affymetrix Data for Demonstration Purpose
affyio 1.54.0 Tools for parsing Affymetrix data files
affylmGUI 1.58.0 GUI for limma Package with Affymetrix Microarrays
affyPLM 1.60.0 Methods for fitting probe-level models
affyQCReport 1.62.0 QC Report Generation for affyBatch objects
akima 0.6-2 Interpolation of Irregularly and Regularly Spaced Data
annaffy 1.56.0 Annotation tools for Affymetrix biological metadata
annmap 1.26.0 Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate 1.62.0 Annotation for microarrays
AnnotationDbi 1.46.0 Manipulation of SQLite-based annotations in Bioconductor
AnnotationFilter 1.8.0 Facilities for Filtering Bioconductor Annotation Resources
ape 5.3 Analyses of Phylogenetics and Evolution
arm 1.10-1 Data Analysis Using Regression and Multilevel/Hierarchical Models
aroma.affymetrix 3.2.0 Analysis of Large Affymetrix Microarray Data Sets
aroma.apd 0.6.0 A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
aroma.core 3.2.0 Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
aroma.light 3.14.0 Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
askpass 1.1 Safe Password Entry for R, Git, and SSH
assertthat 0.2.1 Easy Pre and Post Assertions
backports 1.1.4 Reimplementations of Functions Introduced Since R-3.0.0
base 3.6.0 The R Base Package
base64 2.0 Base64 Encoder and Decoder
base64enc 0.1-3 Tools for base64 encoding
BaSTA 1.9.4 Age-Specific Survival Analysis from Incomplete Capture-Recapture/Recovery Data
BatchJobs 1.8 Batch Computing with R
bayesplot 1.7.0 Plotting for Bayesian Models
BBmisc 1.11 Miscellaneous Helper Functions for B. Bischl
beachmat 2.0.0 Compiling Bioconductor to Handle Each Matrix Type
beadarray 2.34.0 Quality assessment and low-level analysis for Illumina BeadArray data
beadarrayExampleData 1.22.0 Example data for the beadarray package
BeadDataPackR 1.36.0 Compression of Illumina BeadArray data
beanplot 1.2 Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
BH 1.69.0-1 Boost C++ Header Files
BiasedUrn 1.07 Biased Urn Model Distributions
bibtex 0.4.2 Bibtex Parser
bio3d 2.3-4 Biological Structure Analysis
Biobase 2.44.0 Biobase: Base functions for Bioconductor
BiocFileCache 1.8.0 Manage Files Across Sessions
BiocGenerics 0.30.0 S4 generic functions used in Bioconductor
BiocParallel 1.18.0 Bioconductor facilities for parallel evaluation
biomaRt 2.40.1 Interface to BioMart databases (i.e. Ensembl)
Biostrings 2.52.0 Efficient manipulation of biological strings
biovizBase 1.32.0 Basic graphic utilities for visualization of genomic data.
bit 1.1-14 A Class for Vectors of 1-Bit Booleans
bit64 0.9-7 A S3 Class for Vectors of 64bit Integers
bitops 1.0-6 Bitwise Operations
blob 1.1.1 A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
blockmodeling 0.3.4 Generalized and Classical Blockmodeling of Valued Networks
boot 1.3-22 Bootstrap Functions (Originally by Angelo Canty for S)
brew 1.0-6 Templating Framework for Report Generation
broom 0.5.2 Convert Statistical Analysis Objects into Tidy Tibbles
BSgenome 1.52.0 Software infrastructure for efficient representation of full genomes and their SNPs
BSgenome.Hsapiens.UCSC.hg19 1.4.0 Full genome sequences for Homo sapiens (UCSC version hg19)
bsseq 1.20.0 Analyze, manage and store bisulfite sequencing data
bumphunter 1.26.0 Bump Hunter
callr 3.2.0 Call R from R
car 3.0-3 Companion to Applied Regression
carData 3.0-2 Companion to Applied Regression Data Sets
caret 6.0-84 Classification and Regression Training
Category 2.50.0 Category Analysis
caTools 1.17.1.2 Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
CDM 7.3-17 Cognitive Diagnosis Modeling
cellranger 1.1.0 Translate Spreadsheet Cell Ranges to Rows and Columns
ChAMP 2.14.0 Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
ChAMPdata 2.16.0 Data Packages for ChAMP package
checkmate 1.9.4 Fast and Versatile Argument Checks
class 7.3-15 Functions for Classification
classInt 0.3-3 Choose Univariate Class Intervals
cli 1.1.0 Helpers for Developing Command Line Interfaces
clipr 0.6.0 Read and Write from the System Clipboard
clisymbols 1.2.0 Unicode Symbols at the R Prompt
clue 0.3-57 Cluster Ensembles
cluster 2.0.8 "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
cmprsk 2.2-8 Subdistribution Analysis of Competing Risks
coda 0.19-3 Output Analysis and Diagnostics for MCMC
codetools 0.2-16 Code Analysis Tools for R
colorRamps 2.3 Builds color tables
colorspace 1.4-1 A Toolbox for Manipulating and Assessing Colors and Palettes
colourpicker 1.0 A Colour Picker Tool for Shiny and for Selecting Colours in Plots
combinat 0.0-8 combinatorics utilities
compiler 3.6.0 The R Compiler Package
copula 0.999-19.1 Multivariate Dependence with Copulas
copynumber 1.24.0 Segmentation of single- and multi-track copy number data by penalized least squares regression.
corpcor 1.6.9 Efficient Estimation of Covariance and (Partial) Correlation
corrplot 0.84 Visualization of a Correlation Matrix
crayon 1.3.4 Colored Terminal Output
crosstalk 1.0.0 Inter-Widget Interactivity for HTML Widgets
curl 3.3 A Modern and Flexible Web Client for R
data.table 1.12.2 Extension of data.frame
datasets 3.6.0 The R Datasets Package
DBI 1.0.0 R Database Interface
dbplyr 1.4.0 A 'dplyr' Back End for Databases
DelayedArray 0.10.0 A unified framework for working transparently with on-disk and in-memory array-like datasets
DelayedMatrixStats 1.6.0 Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
deldir 0.1-16 Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend 1.12.0 Extending 'dendrogram' Functionality in R
DEoptimR 1.0-8 Differential Evolution Optimization in Pure R
desc 1.2.0 Manipulate DESCRIPTION Files
DESeq 1.36.0 Differential gene expression analysis based on the negative binomial distribution
DESeq2 1.24.0 Differential gene expression analysis based on the negative binomial distribution
Design 2.3-0 Design Package
devtools 2.0.2 Tools to Make Developing R Packages Easier
DEXSeq 1.30.0 Inference of differential exon usage in RNA-Seq
dichromat 2.0-0 Color Schemes for Dichromats
digest 0.6.20 Create Compact Hash Digests of R Objects
diptest 0.75-7 Hartigan's Dip Test Statistic for Unimodality - Corrected
distr 2.8.0 Object Oriented Implementation of Distributions
distrEx 2.8.0 Extensions of Package 'distr'
DMRcate 1.20.0 Methylation array and sequencing spatial analysis methods
DMRcatedata 1.20.0 Data Package for DMRcate package
DNAcopy 1.58.0 DNA copy number data analysis
doMC 1.3.5 Foreach Parallel Adaptor for 'parallel'
doParallel 1.0.14 Foreach Parallel Adaptor for the 'parallel' Package
doRNG 1.7.1 Generic Reproducible Parallel Backend for 'foreach' Loops
dotCall64 1.0-0 Enhanced Foreign Function Interface Supporting Long Vectors
dplyr 0.8.1 A Grammar of Data Manipulation
DSS 2.32.0 Dispersion shrinkage for sequencing data
DT 0.6 A Wrapper of the JavaScript Library 'DataTables'
dygraphs 1.1.1.6 Interface to 'Dygraphs' Interactive Time Series Charting Library
dynamicTreeCut 1.63-1 Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
DynDoc 1.62.0 Dynamic document tools
e1071 1.7-2 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
easyRNASeq 2.20.0 Count summarization and normalization for RNA-Seq data
EBSeq 1.24.0 An R package for gene and isoform differential expression analysis of RNA-seq data
edgeR 3.26.5 Empirical Analysis of Digital Gene Expression Data in R
effects 4.1-1 Effect Displays for Linear, Generalized Linear, and Other Models
ellipse 0.4.1 Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
ellipsis 0.1.0 Tools for Working with ...
ensembldb 2.8.0 Utilities to create and use Ensembl-based annotation databases
Epi 2.37 A Package for Statistical Analysis in Epidemiology
erer 2.5 Empirical Research in Economics with R
estimability 1.3 Tools for Assessing Estimability of Linear Predictions
etm 1.0.5 Empirical Transition Matrix
evaluate 0.14 Parsing and Evaluation Tools that Provide More Details than the Default
evd 2.3-3 Functions for Extreme Value Distributions
expm 0.999-4 Matrix Exponential, Log, 'etc'
extrafont 0.17 Tools for using fonts
extrafontdb 1.0 Package for holding the database for the extrafont package
FactoMineR 1.42 Multivariate Exploratory Data Analysis and Data Mining
fail 1.3 File Abstraction Interface Layer (FAIL)
fansi 0.4.0 ANSI Control Sequence Aware String Functions
fastcluster 1.1.25 Fast Hierarchical Clustering Routines for R and 'Python'
fastICA 1.2-1 FastICA Algorithms to Perform ICA and Projection Pursuit
fastmatch 1.1-0 Fast match() function
FDb.InfiniumMethylation.hg19 2.2.0 Annotation package for Illumina Infinium DNA methylation probes
fdrtool 1.2.15 Estimation of (Local) False Discovery Rates and Higher Criticism
FEM 3.12.0 Identification of Functional Epigenetic Modules
fields 9.8-3 Tools for Spatial Data
fit.models 0.5-14 Compare Fitted Models
flashClust 1.01-2 Implementation of optimal hierarchical clustering
flexmix 2.3-15 Flexible Mixture Modeling
forcats 0.4.0 Tools for Working with Categorical Variables (Factors)
foreach 1.4.4 Provides Foreach Looping Construct for R
foreign 0.8-71 Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...
formatR 1.6 Format R Code Automatically
Formula 1.2-3 Extended Model Formulas
fpc 2.2-3 Flexible Procedures for Clustering
fs 1.3.1 Cross-Platform File System Operations Based on 'libuv'
futile.logger 1.4.3 A Logging Utility for R
futile.options 1.0.1 Futile Options Management
future 1.13.0 Unified Parallel and Distributed Processing in R for Everyone
gam 1.16.1 Generalized Additive Models
gamlss 5.1-4 Generalised Additive Models for Location Scale and Shape
gamlss.data 5.1-4 GAMLSS Data
gamlss.dist 5.1-4 Distributions for Generalized Additive Models for Location Scale and Shape
gamlss.mx 4.3-5 Fitting Mixture Distributions with GAMLSS
gamlss.nl 4.1-0 Fitting non linear parametric GAMLSS models
gcrma 2.56.0 Background Adjustment Using Sequence Information
gdalUtils 2.0.1.14 Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities
gdata 2.18.0 Various R Programming Tools for Data Manipulation
gdtools 0.1.8 Utilities for Graphical Rendering
genefilter 1.66.0 genefilter: methods for filtering genes from high-throughput experiments
geneLenDataBase 1.20.0 Lengths of mRNA transcripts for a number of genomes
GeneNet 1.2.13 Modeling and Inferring Gene Networks
geneplotter 1.62.0 Graphics related functions for Bioconductor
generics 0.0.2 Common S3 Generics not Provided by Base R Methods Related to Model Fitting
genetics 1.3.8.1.2 Population Genetics
GenomeGraphs 1.44.0 Plotting genomic information from Ensembl
GenomeInfoDb 1.20.0 Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
GenomeInfoDbData 1.2.1 Species and taxonomy ID look up tables used by GenomeInfoDb
genomeIntervals 1.40.0 Operations on genomic intervals
GenomicAlignments 1.20.1 Representation and manipulation of short genomic alignments
GenomicFeatures 1.36.3 Conveniently import and query gene models
GenomicRanges 1.36.0 Representation and manipulation of genomic intervals
GEOquery 2.52.0 Get data from NCBI Gene Expression Omnibus (GEO)
GGally 1.4.0 Extension to 'ggplot2'
ggplot2 3.2.0 Create Elegant Data Visualisations Using the Grammar of Graphics
ggrepel 0.8.1 Automatically Position Non-Overlapping Text Labels with 'ggplot2'
ggridges 0.5.1 Ridgeline Plots in 'ggplot2'
gh 1.0.1 'GitHub' 'API'
git2r 0.25.2 Provides Access to Git Repositories
GJRM 0.2 Generalised Joint Regression Modelling
glmnet 2.0-18 Lasso and Elastic-Net Regularized Generalized Linear Models
globals 0.12.4 Identify Global Objects in R Expressions
globaltest 5.38.0 Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
glue 1.3.1 Interpreted String Literals
gmodels 2.18.1 Various R Programming Tools for Model Fitting
gmp 0.5-13.5 Multiple Precision Arithmetic
goseq 1.36.0 Gene Ontology analyser for RNA-seq and other length biased data
GOstats 2.50.0 Tools for manipulating GO and microarrays
gower 0.2.1 Gower's Distance
gplots 3.0.1.1 Various R Programming Tools for Plotting Data
graph 1.62.0 graph: A package to handle graph data structures
graphics 3.6.0 The R Graphics Package
grDevices 3.6.0 The R Graphics Devices and Support for Colours and Fonts
grid 3.6.0 The Grid Graphics Package
gridExtra 2.3 Miscellaneous Functions for "Grid" Graphics
GSEABase 1.46.0 Gene set enrichment data structures and methods
gsl 2.1-6 Wrapper for the Gnu Scientific Library
gsmoothr 0.1.7 Smoothing tools
gtable 0.3.0 Arrange 'Grobs' in Tables
gtools 3.8.1 Various R Programming Tools
Gviz 1.28.0 Plotting data and annotation information along genomic coordinates
HAC 1.0-5 Estimation, Simulation and Visualization of Hierarchical Archimedean Copulae (HAC)
haplo.stats 1.7.9 Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
haven 2.1.0 Import and Export 'SPSS', 'Stata' and 'SAS' Files
HDF5Array 1.12.1 HDF5 backend for DelayedArray objects
hexbin 1.27.3 Hexagonal Binning Routines
HI 0.4 Simulation from distributions supported by nested hyperplanes
highr 0.8 Syntax Highlighting for R Source Code
Hmisc 4.2-0 Harrell Miscellaneous
hms 0.4.2 Pretty Time of Day
HotDeckImputation 1.1.0 Hot Deck Imputation Methods for Missing Data
htmlTable 1.13.1 Advanced Tables for Markdown/HTML
htmltools 0.3.6 Tools for HTML
htmlwidgets 1.3 HTML Widgets for R
httpuv 1.5.1 HTTP and WebSocket Server Library
httr 1.4.0 Tools for Working with URLs and HTTP
hwriter 1.3.2 HTML Writer - Outputs R objects in HTML format
igraph 1.2.4.1 Network Analysis and Visualization
IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0 Annotation for Illumina's 450k methylation arrays
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 0.6.0 Annotation for Illumina's EPIC methylation arrays
IlluminaHumanMethylationEPICanno.ilm10b4.hg19 0.6.0 Annotation for Illumina's EPIC methylation arrays
IlluminaHumanMethylationEPICmanifest 0.3.0 Manifest for Illumina's EPIC methylation arrays
illuminaio 0.26.0 Parsing Illumina Microarray Output Files
impute 1.58.0 impute: Imputation for microarray data
ini 0.3.1 Read and Write '.ini' Files
inline 0.3.15 Functions to Inline C, C++, Fortran Function Calls from R
intervals 0.15.1 Tools for Working with Points and Intervals
ipred 0.9-9 Improved Predictors
IRanges 2.18.1 Foundation of integer range manipulation in Bioconductor
ISOcodes 2019.04.22 Selected ISO Codes
isva 1.9 Independent Surrogate Variable Analysis
iterators 1.0.10 Provides Iterator Construct for R
JADE 2.0-1 Blind Source Separation Methods Based on Joint Diagonalization and Some BSS Performance Criteria
jsonlite 1.6 A Robust, High Performance JSON Parser and Generator for R
kdecopula 0.9.2 Kernel Smoothing for Bivariate Copula Densities
kernlab 0.9-27 Kernel-Based Machine Learning Lab
KernSmooth 2.23-15 Functions for Kernel Smoothing Supporting Wand & Jones (1995)
knitr 1.23 A General-Purpose Package for Dynamic Report Generation in R
kohonen 3.0.8 Supervised and Unsupervised Self-Organising Maps
kpmt 0.1.0 Known Population Median Test
labeling 0.3 Axis Labeling
lambda.r 1.2.3 Modeling Data with Functional Programming
later 0.8.0 Utilities for Delaying Function Execution
lattice 0.20-38 Trellis Graphics for R
latticeExtra 0.6-28 Extra Graphical Utilities Based on Lattice
lava 1.6.5 Latent Variable Models
lazyeval 0.2.2 Lazy (Non-Standard) Evaluation
leafem 0.0.1 'leaflet' Extensions for 'mapview'
leaflet 2.0.2 Create Interactive Web Maps with the JavaScript 'Leaflet' Library
leafpop 0.0.1 Include Tables, Images and Graphs in Leaflet Pop-Ups
leaps 3.0 Regression Subset Selection
LearnBayes 2.15.1 Functions for Learning Bayesian Inference
limma 3.40.2 Linear Models for Microarray Data
listenv 0.7.0 Environments Behaving (Almost) as Lists
lme4 1.1-21 Linear Mixed-Effects Models using 'Eigen' and S4
lmtest 0.9-37 Testing Linear Regression Models
locfit 1.5-9.1 Local Regression, Likelihood and Density Estimation.
longitudinal 1.1.12 Analysis of Multiple Time Course Data
loo 2.1.0 Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
lpSolve 5.6.13.1 Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
LSD 4.0-0 Lots of Superior Depictions
ltm 1.1-1 Latent Trait Models under IRT
lubridate 1.7.4 Make Dealing with Dates a Little Easier
lumi 2.36.0 BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
lwgeom 0.1-7 Bindings to Selected 'liblwgeom' Functions for Simple Features
made4 1.58.0 Multivariate analysis of microarray data using ADE4
magic 1.5-9 Create and Investigate Magic Squares
magrittr 1.5 A Forward-Pipe Operator for R
manipulateWidget 0.10.0 Add Even More Interactivity to Interactive Charts
maps 3.3.0 Draw Geographical Maps
maptools 0.9-5 Tools for Handling Spatial Objects
maptree 1.4-7 Mapping, pruning, and graphing tree models
mapview 2.7.0 Interactive Viewing of Spatial Data in R
markdown 0.9 'Markdown' Rendering for R
marray 1.62.0 Exploratory analysis for two-color spotted microarray data
MASS 7.3-51.4 Support Functions and Datasets for Venables and Ripley's MASS
Matrix 1.2-17 Sparse and Dense Matrix Classes and Methods
matrixcalc 1.0-3 Collection of functions for matrix calculations
MatrixModels 0.4-1 Modelling with Sparse And Dense Matrices
matrixStats 0.54.0 Functions that Apply to Rows and Columns of Matrices (and to Vectors)
mclust 5.4.4 Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
mcmc 0.9-6 Markov Chain Monte Carlo
memoise 1.1.0 Memoisation of Functions
metafor 2.1-0 Meta-Analysis Package for R
methods 3.6.0 Formal Methods and Classes
methylumi 2.30.0 Handle Illumina methylation data
mgcv 1.8-28 Mixed GAM Computation Vehicle with Automatic Smoothness Estimation
mime 0.6 Map Filenames to MIME Types
minfi 1.30.0 Analyze Illumina Infinium DNA methylation arrays
miniUI 0.1.1.1 Shiny UI Widgets for Small Screens
minqa 1.2.4 Derivative-free optimization algorithms by quadratic approximation
missMethyl 1.18.0 Analysing Illumina HumanMethylation BeadChip Data
mitools 2.4 Tools for Multiple Imputation of Missing Data
mlr 2.14.0 Machine Learning in R
mnormt 1.5-5 The Multivariate Normal and t Distributions
ModelMetrics 1.2.2 Rapid Calculation of Model Metrics
modelr 0.1.4 Modelling Functions that Work with the Pipe
modeltools 0.2-22 Tools and Classes for Statistical Models
msm 1.6.7 Multi-State Markov and Hidden Markov Models in Continuous Time
mstate 0.2.11 Data Preparation, Estimation and Prediction in Multi-State Models
multcomp 1.4-10 Simultaneous Inference in General Parametric Models
multtest 2.40.0 Resampling-based multiple hypothesis testing
munsell 0.5.0 Utilities for Using Munsell Colours
mvtnorm 1.0-11 Multivariate Normal and t Distributions
network 1.15 Classes for Relational Data
nleqslv 3.3.2 Solve Systems of Nonlinear Equations
nlme 3.1-139 Linear and Nonlinear Mixed Effects Models
nloptr 1.2.1 R Interface to NLopt
NLP 0.2-0 Natural Language Processing Infrastructure
nnet 7.3-12 Feed-Forward Neural Networks and Multinomial Log-Linear Models
nor1mix 1.3-0 Normal aka Gaussian (1-d) Mixture Models (S3 Classes and Methods)
numDeriv 2016.8-1.1 Accurate Numerical Derivatives
nutshell 2.0 Data for "R in a Nutshell"
nutshell.audioscrobbler 1.0 Audioscrobbler data for "R in a Nutshell"
nutshell.bbdb 1.0 Baseball Database for "R in a Nutshell"
OPE 0.7 Outer-product emulator
openssl 1.4 Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
openxlsx 4.1.0.1 Read, Write and Edit XLSX Files
packrat 0.5.0 A Dependency Management System for Projects and their R Package Dependencies
panelAR 0.1 Estimation of Linear AR(1) Panel Data Models with Cross-Sectional Heteroskedasticity and/or Correlation
parallel 3.6.0 Support for Parallel computation in R
parallelMap 1.4 Unified Interface to Parallelization Back-Ends
ParamHelpers 1.12 Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
parcor 0.2-6 Regularized estimation of partial correlation matrices
pbkrtest 0.4-7 Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
pcaPP 1.9-73 Robust PCA by Projection Pursuit
pegas 0.11 Population and Evolutionary Genetics Analysis System
permute 0.9-5 Functions for Generating Restricted Permutations of Data
phangorn 2.5.5 Phylogenetic Reconstruction and Analysis
pillar 1.4.1 Coloured Formatting for Columns
pixmap 0.4-11 Bitmap Images (``Pixel Maps'')
pkgbuild 1.0.3 Find Tools Needed to Build R Packages
pkgconfig 2.0.2 Private Configuration for 'R' Packages
pkgload 1.0.2 Simulate Package Installation and Attach
pkgmaker 0.27 Development Utilities for R Packages
plogr 0.2.0 The 'plog' C++ Logging Library
plotly 4.9.0 Create Interactive Web Graphics via 'plotly.js'
pls 2.7-1 Partial Least Squares and Principal Component Regression
plyr 1.8.4 Tools for Splitting, Applying and Combining Data
png 0.1-7 Read and write PNG images
poLCA 1.4.1 Polytomous variable Latent Class Analysis
polspline 1.1.14 Polynomial Spline Routines
polycor 0.7-9 Polychoric and Polyserial Correlations
poweRlaw 0.70.2 Analysis of Heavy Tailed Distributions
ppls 1.6-1.1 Penalized Partial Least Squares
prabclus 2.3-1 Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data
pracma 2.2.5 Practical Numerical Math Functions
praise 1.0.0 Praise Users
preprocessCore 1.46.0 A collection of pre-processing functions
prettydoc 0.2.1 Creating Pretty Documents from R Markdown
prettyunits 1.0.2 Pretty, Human Readable Formatting of Quantities
processx 3.3.1 Execute and Control System Processes
prodlim 2018.04.18 Product-Limit Estimation for Censored Event History Analysis
progress 1.2.2 Terminal Progress Bars
promises 1.0.1 Abstractions for Promise-Based Asynchronous Programming
ProtGenerics 1.16.0 S4 generic functions for Bioconductor proteomics infrastructure
proto 1.0.0 Prototype Object-Based Programming
proxyC 0.1.5 Computes Proximity in Large Sparse Matrices
ps 1.3.0 List, Query, Manipulate System Processes
PSCBS 0.65.0 Analysis of Parent-Specific DNA Copy Numbers
pspline 1.0-18 Penalized Smoothing Splines
psych 1.8.12 Procedures for Psychological, Psychometric, and Personality Research
purrr 0.3.2 Functional Programming Tools
qrng 0.0-5 (Randomized) Quasi-Random Number Generators
quadprog 1.5-7 Functions to Solve Quadratic Programming Problems
quanteda 1.5.1 Quantitative Analysis of Textual Data
quantmod 0.4-14 Quantitative Financial Modelling Framework
quantreg 5.41 Quantile Regression
qvalue 2.16.0 Q-value estimation for false discovery rate control
R.cache 0.13.0 Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
R.devices 2.16.0 Unified Handling of Graphics Devices
R.filesets 2.13.0 Easy Handling of and Access to Files Organized in Structured Directories
R.huge 0.9.0 Methods for Accessing Huge Amounts of Data [deprecated]
R.methodsS3 1.7.1 S3 Methods Simplified
R.oo 1.22.0 R Object-Oriented Programming with or without References
R.rsp 0.43.1 Dynamic Generation of Scientific Reports
R.utils 2.9.0 Various Programming Utilities
R2HTML 2.3.2 HTML Exportation for R Objects
R2jags 0.5-7 Using R to Run 'JAGS'
R2WinBUGS 2.1-21 Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
R6 2.4.0 Encapsulated Classes with Reference Semantics
randomForest 4.6-14 Breiman and Cutler's Random Forests for Classification and Regression
rappdirs 0.3.1 Application Directories: Determine Where to Save Data, Caches, and Logs
raster 2.9-5 Geographic Data Analysis and Modeling
RBGL 1.60.0 An interface to the BOOST graph library
rcmdcheck 1.3.3 Run 'R CMD check' from 'R' and Capture Results
RColorBrewer 1.1-2 ColorBrewer Palettes
Rcpp 1.0.1 Seamless R and C++ Integration
RcppArmadillo 0.9.500.2.0 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library
RcppEigen 0.3.3.5.0 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
RcppGSL 0.3.6 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
RcppParallel 4.4.3 Parallel Programming Tools for 'Rcpp'
RcppRoll 0.3.0 Efficient Rolling / Windowed Operations
RCurl 1.95-4.12 General Network (HTTP/FTP/...) Client Interface for R
readr 1.3.1 Read Rectangular Text Data
readxl 1.3.1 Read Excel Files
recipes 0.1.5 Preprocessing Tools to Create Design Matrices
registry 0.5-1 Infrastructure for R Package Registries
relaimpo 2.2-3 Relative Importance of Regressors in Linear Models
rematch 1.0.1 Match Regular Expressions with a Nicer 'API'
remotes 2.0.4 R Package Installation from Remote Repositories, Including 'GitHub'
Repitools 1.30.0 Epigenomic tools
reprex 0.3.0 Prepare Reproducible Example Code via the Clipboard
reshape 0.8.8 Flexibly Reshape Data
reshape2 1.4.3 Flexibly Reshape Data: A Reboot of the Reshape Package
reticulate 1.13 Interface to 'Python'
rgdal 1.4-4 Bindings for the 'Geospatial' Data Abstraction Library
rgeos 0.4-3 Interface to Geometry Engine - Open Source ('GEOS')
rgl 0.100.24 3D Visualization Using OpenGL
Rglpk 0.6-4 R/GNU Linear Programming Kit Interface
Rgraphviz 2.28.0 Provides plotting capabilities for R graph objects
rhdf5 2.28.0 R Interface to HDF5
Rhdf5lib 1.6.0 hdf5 library as an R package
Rhtslib 1.16.1 HTSlib high-throughput sequencing library as an R package
Ringo 1.48.0 R Investigation of ChIP-chip Oligoarrays
rio 0.5.16 A Swiss-Army Knife for Data I/O
rjags 4-8 Bayesian Graphical Models using MCMC
RJSONIO 1.3-1.2 Serialize R Objects to JSON, JavaScript Object Notation
rlang 0.3.4 Functions for Base Types and Core R and 'Tidyverse' Features
rlecuyer 0.3-4 R Interface to RNG with Multiple Streams
rlist 0.4.6.1 A Toolbox for Non-Tabular Data Manipulation
rmarkdown 1.13 Dynamic Documents for R
Rmpfr 0.7-2 R MPFR - Multiple Precision Floating-Point Reliable
Rmpi 0.6-9 Interface (Wrapper) to MPI (Message-Passing Interface)
rms 5.1-3.1 Regression Modeling Strategies
RMySQL 0.10.17 Database Interface and 'MySQL' Driver for R
RNetCDF 1.9-1 Interface to NetCDF Datasets
rngtools 1.4 Utility Functions for Working with Random Number Generators
robust 0.4-18 Port of the S+ "Robust Library"
robustbase 0.93-5 Basic Robust Statistics
ROC 1.60.0 utilities for ROC, with uarray focus
rpart 4.1-15 Recursive Partitioning and Regression Trees
RPMM 1.25 Recursively Partitioned Mixture Model
rprojroot 1.3-2 Finding Files in Project Subdirectories
rrcov 1.4-7 Scalable Robust Estimators with High Breakdown Point
Rsamtools 2.0.0 Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsconnect 0.8.13 Deployment Interface for R Markdown Documents and Shiny Applications
Rsolnp 1.16 General Non-Linear Optimization
RSpectra 0.15-0 Solvers for Large-Scale Eigenvalue and SVD Problems
RSQLite 2.1.1 'SQLite' Interface for R
rstan 2.18.2 R Interface to Stan
rstanarm 2.18.2 Bayesian Applied Regression Modeling via Stan
rstantools 1.5.1 Tools for Developing R Packages Interfacing with 'Stan'
rstudioapi 0.10 Safely Access the RStudio API
Rsubread 1.34.4 Subread Sequence Alignment and Counting for R
rtracklayer 1.44.0 R interface to genome annotation files and the UCSC genome browser
Rttf2pt1 1.3.7 'ttf2pt1' Program
ruv 0.9.7 Detect and Remove Unwanted Variation using Negative Controls
rvest 0.3.4 Easily Harvest (Scrape) Web Pages
S4Vectors 0.22.0 Foundation of vector-like and list-like containers in Bioconductor
saemix 2.2 Stochastic Approximation Expectation Maximization (SAEM) Algorithm
sampling 2.8 Survey Sampling
sandwich 2.5-1 Robust Covariance Matrix Estimators
satellite 1.0.1 Handling and Manipulating Remote Sensing Data
scales 1.0.0 Scale Functions for Visualization
scam 1.2-4 Shape Constrained Additive Models
scatterplot3d 0.3-41 3D Scatter Plot
schoolmath 0.4 Functions and datasets for math used in school
scrime 1.3.5 Analysis of High-Dimensional Categorical Data Such as SNP Data
segmented 0.5-4.0 Regression Models with Break-Points / Change-Points Estimation
selectr 0.4-1 Translate CSS Selectors to XPath Expressions
sendmailR 1.2-1 send email using R
seqinr 3.4-5 Biological Sequences Retrieval and Analysis
seqLogo 1.50.0 Sequence logos for DNA sequence alignments
sessioninfo 1.1.1 R Session Information
sf 0.7-4 Simple Features for R
sfsmisc 1.1-4 Utilities from 'Seminar fuer Statistik' ETH Zurich
shiny 1.3.2 Web Application Framework for R
shinyjs 1.0 Easily Improve the User Experience of Your Shiny Apps in Seconds
shinystan 2.5.0 Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
shinythemes 1.1.2 Themes for Shiny
ShortRead 1.42.0 FASTQ input and manipulation
siggenes 1.58.0 Multiple Testing using SAM and Efron's Empirical Bayes Approaches
simpleaffy 2.60.0 Very simple high level analysis of Affymetrix data
slam 0.1-45 Sparse Lightweight Arrays and Matrices
sn 1.5-4 The Skew-Normal and Related Distributions Such as the Skew-t
sna 2.4 Tools for Social Network Analysis
snow 0.4-3 Simple Network of Workstations
SnowballC 0.6.0 Snowball Stemmers Based on the C 'libstemmer' UTF-8 Library
snowfall 1.84-6.1 Easier cluster computing (based on snow).
softImpute 1.4 Matrix Completion via Iterative Soft-Thresholded SVD
sourcetools 0.1.7 Tools for Reading, Tokenizing and Parsing R Code
sp 1.3-1 Classes and Methods for Spatial Data
spacyr 1.2 Wrapper to the 'spaCy' 'NLP' Library
spam 2.2-2 SPArse Matrix
SparseM 1.77 Sparse Linear Algebra
spatial 7.3-11 Functions for Kriging and Point Pattern Analysis
spData 0.3.0 Datasets for Spatial Analysis
spdep 1.1-2 Spatial Dependence: Weighting Schemes, Statistics and Models
splines 3.6.0 Regression Spline Functions and Classes
SQUAREM 2017.10-1 Squared Extrapolation Methods for Accelerating EM-Like Monotone Algorithms
stabledist 0.7-1 Stable Distribution Functions
StanHeaders 2.18.1 C++ Header Files for Stan
startupmsg 0.9.6 Utilities for Start-Up Messages
statmod 1.4.32 Statistical Modeling
statnet.common 4.3.0 Common R Scripts and Utilities Used by the Statnet Project Software
stats 3.6.0 The R Stats Package
stats4 3.6.0 Statistical Functions using S4 Classes
stopwords 1.0 Multilingual Stopword Lists
stringdist 0.9.5.2 Approximate String Matching and String Distance Functions
stringi 1.4.3 Character String Processing Facilities
stringr 1.4.0 Simple, Consistent Wrappers for Common String Operations
SummarizedExperiment 1.14.0 SummarizedExperiment container
survey 3.36 Analysis of Complex Survey Samples
survival 2.44-1.1 Survival Analysis
sva 3.32.1 Surrogate Variable Analysis
svglite 1.2.2 An 'SVG' Graphics Device
sys 3.2 Powerful and Reliable Tools for Running System Commands in R
systemfit 1.1-22 Estimating Systems of Simultaneous Equations
TAM 3.2-24 Test Analysis Modules
tcltk 3.6.0 Tcl/Tk Interface
testthat 2.1.1 Unit Testing for R
tgp 2.4-14 Bayesian Treed Gaussian Process Models
TH.data 1.0-10 TH's Data Archive
threejs 0.3.1 Interactive 3D Scatter Plots, Networks and Globes
tibble 2.1.2 Simple Data Frames
tidyr 0.8.3 Easily Tidy Data with 'spread()' and 'gather()' Functions
tidyselect 0.2.5 Select from a Set of Strings
tidyverse 1.2.1 Easily Install and Load the 'Tidyverse'
timeDate 3043.102 Rmetrics - Chronological and Calendar Objects
tinytex 0.13 Helper Functions to Install and Maintain 'TeX Live', and Compile 'LaTeX' Documents
tkrplot 0.0-24 TK Rplot
tm 0.7-6 Text Mining Package
tmap 2.2 Thematic Maps
tmaptools 2.0-1 Thematic Map Tools
tools 3.6.0 Tools for Package Development
topicmodels 0.2-8 Topic Models
truncnorm 1.0-8 Truncated Normal Distribution
trust 0.1-7 Trust Region Optimization
trustOptim 0.8.6.2 Trust Region Optimization for Nonlinear Functions with Sparse Hessians
tseries 0.10-47 Time Series Analysis and Computational Finance
TTR 0.23-4 Technical Trading Rules
TxDb.Hsapiens.UCSC.hg19.knownGene 3.2.2 Annotation package for TxDb object(s)
udunits2 0.13 Udunits-2 Bindings for R
units 0.6-3 Measurement Units for R Vectors
urca 1.3-0 Unit Root and Cointegration Tests for Time Series Data
usethis 1.5.0 Automate Package and Project Setup
utf8 1.1.4 Unicode Text Processing
utils 3.6.0 The R Utils Package
uuid 0.1-2 Tools for generating and handling of UUIDs
V8 2.3 Embedded JavaScript Engine for R
VariantAnnotation 1.30.1 Annotation of Genetic Variants
vctrs 0.1.0 Vector Helpers
vegan 2.5-5 Community Ecology Package
VGAM 1.1-1 Vector Generalized Linear and Additive Models
VineCopula 2.1.8 Statistical Inference of Vine Copulas
viridis 0.5.1 Default Color Maps from 'matplotlib'
viridisLite 0.3.0 Default Color Maps from 'matplotlib' (Lite Version)
vsn 3.52.0 Variance stabilization and calibration for microarray data
wateRmelon 1.28.0 Illumina 450 methylation array normalization and metrics
webshot 0.5.1 Take Screenshots of Web Pages
WGCNA 1.68 Weighted Correlation Network Analysis
whisker 0.3-2 {{mustache}} for R, logicless templating
widgetTools 1.62.0 Creates an interactive tcltk widget
withr 2.1.2 Run Code 'With' Temporarily Modified Global State
xfun 0.7 Miscellaneous Functions by 'Yihui Xie'
XML 3.98-1.20 Tools for Parsing and Generating XML Within R and S-Plus
xml2 1.2.0 Parse XML
xopen 1.0.0 Open System Files, 'URLs', Anything
xps 1.44.0 Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
xtable 1.8-4 Export Tables to LaTeX or HTML
xts 0.11-2 eXtensible Time Series
XVector 0.24.0 Foundation of external vector representation and manipulation in Bioconductor
yaml 2.2.0 Methods to Convert R Data to YAML and Back
zeallot 0.1.0 Multiple, Unpacking, and Destructuring Assignment
zip 2.0.2 Cross-Platform 'zip' Compression
zlibbioc 1.30.0 An R packaged zlib-1.2.5
zoo 1.8-6 S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)