R

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Description

R website  

R is a free software environment for statistical computing and graphics.

Note: File a support ticket to request installation of additional libraries.

Required Modules

modules documentation

Serial

  • R

Parallel (MPI)

  • Rmpi

The "Rmpi" module enables access to the version of R that provides the Rmpi library for large-scale multi-node parallel computations.

See Rmpi documentation for details.

System Variables

  • HPC_R_DIR - installation directory
  • HPC_R_BIN - executable directory
  • HPC_R_LIB - library directory
  • HPC_R_INCLUDE - includes directory

How To Run

R can be run on the command-line (or the batch system) using the 'Rscript myscript.R' or 'R CMD BATCH myscript.R' command. For script development or visualization RStudio GUI application can be used. See the respective documentation for details. For RStudio, load the following modules within your job script before running the rstudio command:

module load gui rstudio
Notes and Warnings
  • Java

rJava users need to load the java module manually with 'module load java/1.7.0_79'

  • TMPDIR

If temporary files are produced the may fill up memory disks on HPG2 nodes and cause node and job failures. Use something like

mkdir -p tmp
export TMPDIR=$(pwd)/tmp

in your job script to prevent this and launch your job from the respective directory and not from your home directory.

  • Tasks vs Cores for parallel runs

Parallel threads in an R job will be bound to the same CPU core even if multiple ntasks are specified in the job script. Use cpus-per-task to use R 'parallel' module correctly. For example, for an 8-thread parallel job use the following resource request in your job script:

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8

See the single-threaded and multi-threaded examples on the Sample SLURM Scripts page for more details.

Job Script Examples

See the R_Job_Script page for R job script examples.

Performance

We have benchmarked our most recent installed R version (3.0.2) built with the included blas/lapack libraries versus the newest (as of April 2015) release 3.2.0 built with Intel MKL libraries on the HiPerGator1 hardware (AMD Abu Dhabi 2.4GHz CPUs) and the Intel Haswell 2.3GHz CPUs we're testing for possible usage in HiPerGator2. The results are presented in the R Benchmark 2.5 table

FAQ

  • Q: When I submit a job using 'parallel' package all threads seem to share a single CPU core instead of running on the separate cores I requested.
    • A: On SLURM you need to use --cpus-per-task to specify the number of available cores. E.g.
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=12

will allow mcapply or other function from the 'parallel' package to run on all requested cores

Rmpi Example

See R MPI Example page for an example of using Rmpi code.

Installed Libraries

Note: Many of the packages in the R library shown below are installed as a part of Bioconductor meta-library. The list is generated from the default R version.

Name Description
a4Base Automated Affymetrix Array Analysis Base Package
a4Classif Automated Affymetrix Array Analysis Classification Package
a4Core Automated Affymetrix Array Analysis Core Package
a4Preproc Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting Automated Affymetrix Array Analysis Reporting Package
abc Tools for Approximate Bayesian Computation (ABC)
abc.data Data Only: Tools for Approximate Bayesian Computation (ABC)
abind Combine Multidimensional Arrays
acepack ace() and avas() for selecting regression transformations
aCGH Classes and functions for Array Comparative Genomic Hybridization data.
actuar Actuarial Functions and Heavy Tailed Distributions
ade4 Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
afex Analysis of Factorial Experiments
affxparser Affymetrix File Parsing SDK
affy Methods for Affymetrix Oligonucleotide Arrays
affydata Affymetrix Data for Demonstration Purpose
affyio Tools for parsing Affymetrix data files
affyPLM Methods for fitting probe-level models
affyQCReport QC Report Generation for affyBatch objects
AGDEX Agreement of Differential Expression Analysis
Agi4x44PreProcess PreProcessing of Agilent 4x44 array data
agricolae Statistical Procedures for Agricultural Research
akima Interpolation of Irregularly and Regularly Spaced Data
AlgDesign Algorithmic Experimental Design
animation A Gallery of Animations in Statistics and Utilities to Create Animations
annaffy Annotation tools for Affymetrix biological metadata
AnnBuilder Bioconductor annotation data package builder
annotate Annotation for microarrays
AnnotationDbi Annotation Database Interface
AnnotationForge Code for Building Annotation Database Packages
aod Analysis of Overdispersed Data
ape Analyses of Phylogenetics and Evolution
aplpack Another Plot PACKage: stem.leaf
arm Data Analysis Using Regression and Multilevel/Hierarchical Models
aroma.affymetrix Analysis of Large Affymetrix Microarray Data Sets
aroma.apd A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
aroma.core Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
aroma.light Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
arrayQualityMetrics Quality metrics report for microarray data sets
asremlPlus Augments the Use of 'Asreml' in Fitting Mixed Models
assertthat Easy pre and post assertions.
aster Aster Models
auteur Bayesian sampler of the trait-evolutionary process
auto3dgm 3-Dimensional Geometric Morphometrics
automap Automatic interpolation package
aws Adaptive Weights Smoothing
awsMethods Class and Methods Definitions for Packages 'aws'
BAMD Bayesian Association Model for Genomic Data with Missing Covariates
base64 Base64 Encoder and Decoder
base64enc Tools for base64 encoding
baseline Baseline Correction of Spectra
batchmeans Consistent Batch Means Estimation of Monte Carlo Standard Errors
batman Bayesian AuTomated Metabolite Analyser for NMR spectra
BayesLogit Logistic Regression
BayesTree Bayesian Additive Regression Trees
baySeq Empirical Bayesian analysis of patterns of differential expression in count data
BB Solving and Optimizing Large-Scale Nonlinear Systems
bdsmatrix Routines for Block Diagonal Symmetric matrices
beadarray Quality assessment and low-level analysis for Illumina BeadArray data
BeadDataPackR Compression of Illumina BeadArray data
beanplot Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
Benchmarking Benchmark and Frontier Analysis Using DEA and SFA
bfast Breaks For Additive Season and Trend (BFAST)
BGLR Bayesian Generalized Linear Regression
BH Boost C++ Header Files
BiasedUrn Biased Urn Model Distributions
BigVAR Dimension Reduction Methods for Multivariate Time Series
binom Binomial Confidence Intervals For Several Parameterizations
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions for Bioconductor
BiocInstaller Install/Update Bioconductor
BiocParallel Bioconductor facilities for parallel evaluation
BioGeoBEARS BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts
biom An interface package (beta) for the BIOM file format.
biomaRt Interface to BioMart databases (e.g. Ensembl
biomod2 Ensemble platform for species distribution modeling
BIOM.utils Utilities for the BIOM (Biological Observation Matrix) Format
Biostrings String objects representing biological sequences
biovizBase Basic graphic utilities for visualization of genomic data.
bit A class for vectors of 1-bit booleans
bitops Bitwise Operations
biwt Functions to compute the biweight mean vector and covariance & correlation matrices
blockmodeling An R package for Generalized and classical blockmodeling of valued networks
BLR Bayesian Linear Regression
bold Interface to Bold Systems 'API'
brew Templating Framework for Report Generation
BSgenome Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
BSgenome.Hsapiens.UCSC.hg19 Full genome sequences for Homo sapiens (UCSC version hg19)
bumphunter Bump Hunter
Cairo R graphics device using cairo graphics library for creating high-quality bitmap (PNG
cairoDevice Cairo-based Graphics Device Driver
calibrate Calibration of Scatterplot and Biplot Axes
camel Calibrated Machine Learning
CAMERA Collection of annotation related methods for mass spectrometry data
caper Comparative Analyses of Phylogenetics and Evolution in R
car Companion to Applied Regression
caret Classification and Regression Training
Category Category Analysis
caTools Tools: moving window statistics
CCA Canonical correlation analysis
cghFLasso Detecting hot spot on CGH array data with fused lasso regression.
chron Chronological Objects which can Handle Dates and Times
Ckmeans.1d.dp Optimal and Fast Univariate k-Means Clustering
cladoRcpp C++ implementations of phylogenetic cladogenesis calculations
clime Constrained L1-minimization for Inverse (covariance) Matrix Estimation
clue Cluster Ensembles
cluster Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al.
clusterGeneration Random Cluster Generation (with Specified Degree of Separation)
CNVtools A package to test genetic association with CNV data
coda Output Analysis and Diagnostics for MCMC
coin Conditional Inference Procedures in a Permutation Test Framework
colorspace Color Space Manipulation
combinat combinatorics utilities
CompQuadForm Distribution function of quadratic forms in normal variables
CompRandFld Composite-Likelihood Based Analysis of Random Fields
corHMM Analysis of Binary Character Evolution
cor.pairwise.tg This package is to do correlation analysis in pairwise for all input samples
corpcor Efficient Estimation of Covariance and (Partial) Correlation
coxme Mixed Effects Cox Models
CpGassoc Association Between Methylation and a Phenotype of Interest
crayon Colored Terminal Output
crlmm Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
CSAR Statistical tools for the analysis of ChIP-seq data
cubature Adaptive multivariate integration over hypercubes
cummeRbund Analysis
curl A Modern and Flexible Web Client for R
d3Network Tools for creating D3 JavaScript network
D3TableFilter A table widget based on D3.js and the "HTML Table Filter Generator"
dae Functions Useful in the Design and ANOVA of Experiments
data.table Extension of Data.frame
DBI R Database Interface
deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
DEoptimR Differential Evolution Optimization in Pure R
DESeq Differential gene expression analysis based on the negative binomial distribution
DESeq2 Differential gene expression analysis based on the negative binomial distribution
deSolve Solvers for Initial Value Problems of Differential Equations (ODE
devtools Tools to Make Developing R Packages Easier
DEXSeq Inference of differential exon usage in RNA-Seq
dfoptim Derivative-Free Optimization
DiagrammeR Create Graph Diagrams and Flowcharts Using R
DiceKriging Kriging Methods for Computer Experiments
dichromat Color Schemes for Dichromats
digest Create Compact Hash Digests of R Objects
diptest Hartigan's Dip Test Statistic for Unimodality - Corrected
dismo Species Distribution Modeling
distillery Method Functions for Confidence Intervals and to Distill Information from an Object
diversitree Comparative Phylogenetic Analyses of Diversification
diveRsity A Comprehensive
dlm Bayesian and Likelihood Analysis of Dynamic Linear Models
DNAcopy DNA copy number data analysis
doBy Groupwise Statistics
doMC Foreach Parallel Adaptor for 'parallel'
doParallel Foreach Parallel Adaptor for the 'parallel' Package
doRNG Generic Reproducible Parallel Backend for foreach Loops
doSNOW Foreach Parallel Adaptor for the 'snow' Package
dplyr A Grammar of Data Manipulation
dse Dynamic Systems Estimation (Time Series Package)
DT A Wrapper of the JavaScript Library 'DataTables'
dummies Create dummy/indicator variables flexibly and efficiently
dygraphs Interface to 'Dygraphs' Interactive Time Series Charting Library
dynamicTreeCut Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
DynDoc Dynamic document tools
e1071 Misc Functions of the Department of Statistics
easyGgplot2 Perform and customize easily a plot with ggplot2
EBSeq An R package for gene and isoform differential expression analysis of RNA-seq data
EDASeq Exploratory Data Analysis and Normalization for RNA-Seq
edgeR Empirical analysis of digital gene expression data in R
eeptools Convenience Functions for Education Data
effects Effect Displays for Linear
eiPack eiPack: Ecological Inference and Higher-Dimension Data Management
eiPackP eiPackP: Ecological Inference and Higher-Dimension Data Management
ellipse Functions for drawing ellipses and ellipse-like confidence regions
elrm Exact Logistic Regression via MCMC
EMMIXskew The EM Algorithm and Skew Mixture Distribution
emplik Empirical Likelihood Ratio for Censored/Truncated Data
emulator Bayesian emulation of computer programs
ENMeval Automated Runs and Evaluations of Ecological Niche Models
ENmix Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip
equate Observed-Score Linking and Equating
eRm Extended Rasch Modeling
estimability Tools for Assessing Estimability of Linear Predictions
evaluate Parsing and Evaluation Tools that Provide More Details than the Default
expm Matrix Exponential
expr.diff.ebseq.tg this package to do differential gene expression analysis on two conditions.
extRemes Extreme Value Analysis
FactoMineR Multivariate Exploratory Data Analysis and Data Mining
fastcluster Fast Hierarchical Clustering Routines for R and Python
fastmatch Fast match() function
fBasics Rmetrics - Markets and Basic Statistics
FD Measuring functional diversity (FD) from multiple traits
fda Functional Data Analysis
FDb.InfiniumMethylation.hg19 Annotation package for Illumina Infinium DNA methylation probes
fdrtool Estimation of (Local) False Discovery Rates and Higher Criticism
ff memory-efficient storage of large data on disk and fast access functions
ffbase Basic Statistical Functions for Package 'ff'
fGarch Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
fields Tools for Spatial Data
FinTS Companion to Tsay (2005) Analysis of Financial Time Series
flashClust Implementation of optimal hierarchical clustering
flexmix Flexible Mixture Modeling
FNN Fast Nearest Neighbor Search Algorithms and Applications
foreach Provides Foreach Looping Construct for R
forecast Forecasting Functions for Time Series and Linear Models
formatR Format R Code Automatically
Formula Extended Model Formulas
fpc Flexible Procedures for Clustering
fracdiff Fractionally differenced ARIMA aka ARFIMA(p
fUnitRoots Trends and Unit Roots
futile.logger A Logging Utility for R
futile.options Futile options management
future A Future API for R
GA Genetic Algorithms
GAabbreviate Abbreviating Items Measures using Genetic Algorithms
gage Generally Applicable Gene-set Enrichment for Pathway Analysis
gageData Auxillary data for gage package
gam Generalized Additive Models
gamm4 Generalized additive mixed models using mgcv and lme4
gbm Generalized Boosted Regression Models
gcrma Background Adjustment Using Sequence Information
gdata Various R Programming Tools for Data Manipulation
gdsfmt R Interface to CoreArray Genomic Data Structure (GDS) Files
gee Generalized Estimation Equation Solver
geepack Generalized Estimating Equation Package
geiger Analysis of Evolutionary Diversification
GenABEL genome-wide SNP association analysis
GenABEL.data Package contains data which is used by GenABEL example and test functions
GeneCycle Identification of Periodically Expressed Genes
genefilter genefilter: methods for filtering genes from high-throughput experiments
GeneNet Modeling and Inferring Gene Networks
geneplotter Graphics related functions for Bioconductor
genetics Population Genetics
GeneticsPed Pedigree and genetic relationship functions
genlasso Path algorithm for generalized lasso problems
GenomeInfoDb Utilities for manipulating chromosome and other 'seqname' identifiers
GenometriCorr Genometric Correlation package
GenomicAlignments Representation and manipulation of short genomic alignments
GenomicFeatures Tools for making and manipulating transcript centric annotations
GenomicRanges Representation and manipulation of genomic intervals and variables defined along a genome
GenSA R Functions for Generalized Simulated Annealing
geometry Mesh Generation and Surface Tesselation
GEOquery Get data from NCBI Gene Expression Omnibus (GEO)
geoR Analysis of Geostatistical Data
geoRglm A Package for Generalised Linear Spatial Models
geosphere Spherical Trigonometry
getopt C-like getopt behavior.
GGally Extension to ggplot2
ggm Functions for graphical Markov models
ggmap Spatial Visualization with ggplot2
ggplot2 An Implementation of the Grammar of Graphics
ggRandomForests Visually Exploring Random Forests
ggvis Interactive Grammar of Graphics
GIGrvg Random Variate Generator for the GIG Distribution
git2r Provides Access to Git Repositories
GLAD Gain and Loss Analysis of DNA
glasso Graphical lasso- estimation of Gaussian graphical models
glmmADMB Generalized Linear Mixed Models using 'AD Model Builder'
glmnet Lasso and Elastic-Net Regularized Generalized Linear Models
globals Identify Global Objects in R Expressions
gmm Generalized Method of Moments and Generalized Empirical Likelihood
gmodels Various R Programming Tools for Model Fitting
gmp Multiple Precision Arithmetic
GO.db A set of annotation maps describing the entire Gene Ontology
goftest Classical Goodness-of-Fit Tests for Univariate Distributions
GOstats Tools for manipulating GO and microarrays.
GPfit Gaussian Processes Modeling
gplots Various R Programming Tools for Plotting Data
GPseq gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments
graph graph: A package to handle graph data structures
gregmisc Greg's Miscellaneous Functions
gridBase Integration of base and grid graphics
gridExtra Miscellaneous Functions for "Grid" Graphics
gridSVG Export 'grid' Graphics as SVG
grofit The package was developed to fit fit many growth curves obtained under different conditions.
GSA Gene set analysis
gsalib Utility Functions For GATK
gsDesign Group Sequential Design
GSEABase Gene set enrichment data structures and methods
gsl wrapper for the Gnu Scientific Library
gsmoothr Smoothing tools
gss General Smoothing Splines
gstat Spatial and Spatio-Temporal Geostatistical Modelling
gsubfn Utilities for strings and function arguments.
gtable Arrange 'Grobs' in Tables
gtools Various R Programming Tools
Gviz Plotting data and annotation information along genomic coordinates
gWidgets gWidgets API for building toolkit-independent
gWidgetsRGtk2 Toolkit implementation of gWidgets for RGtk2
HaploSim Functions to simulate haplotypes
haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
heatmap.plus Heatmap with more sensible behavior.
hexbin Hexagonal Binning Routines
hglm Hierarchical Generalized Linear Models
hglm.data Data for The hglm Package
hgu133plus2.db Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2)
hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2)
hierNet A Lasso for Hierarchical Interactions
highr Syntax Highlighting for R Source Code
HilbertVis Hilbert curve visualization
hisse Hidden State Speciation and Extinction
Hmisc Harrell Miscellaneous
HSAUR2 A Handbook of Statistical Analyses Using R (2nd Edition)
htmltools Tools for HTML
htmlwidgets HTML Widgets for R
httpuv HTTP and WebSocket Server Library
httr Tools for Working with URLs and HTTP
huge High-Dimensional Undirected Graph Estimation
hwriter HTML Writer - Outputs R objects in HTML format
hydroGOF Goodness-of-fit functions for comparison of simulated and observed hydrological time series
hydroTSM Time series management
hyperSpec Work with Hyperspectral Data
Icens NPMLE for Censored and Truncated Data
ICS Tools for Exploring Multivariate Data via ICS/ICA
ICSNP Tools for Multivariate Nonparametrics
igraph Network Analysis and Visualization
IlluminaHumanMethylation450kanno.ilmn12.hg19 Annotation for Illumina's 450k methylation arrays
IlluminaHumanMethylation450kmanifest Annotation for Illumina's 450k methylation arrays
illuminaio Parsing Illumina Microarray Output Files
impute impute: Imputation for microarray data
in2extRemes Into the extRemes Package
INLA Functions which Allow to Perform Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
inline Functions to Inline C
interactiveDisplay Package for enabling powerful shiny web displays of Bioconductor objects
interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects
intergraph Coercion Routines for Network Data Objects
intervals Tools for Working with Points and Intervals
IRanges Infrastructure for manipulating intervals on sequences
irlba Fast Truncated SVD
iterators Provides Iterator Construct for R
itertools Iterator Tools
jpeg Read and write JPEG images
jsonlite A Robust
KEGG.db A set of annotation maps for KEGG
KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGREST Client-side REST access to KEGG
kernlab Kernel-Based Machine Learning Lab
KFAS Kalman Filter and Smoother for Exponential Family State Space Models
klaR Classification and visualization
knitr A General-Purpose Package for Dynamic Report Generation in R
ks Kernel Smoothing
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
lars Least Angle Regression
laser Likelihood Analysis of Speciation/Extinction Rates from Phylogenies
lassoshooting L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting
lattice Trellis Graphics for R
latticeExtra Extra Graphical Utilities Based on Lattice
lavaan Latent Variable Analysis
lazyeval Lazy (Non-Standard) Evaluation
LDcorSV Linkage disequilibrium corrected by the structure and the relatedness
LDna Linkage disequilibrum network analysis (LDna)
LEA LEA: an R package for Landscape and Ecological Association Studies
leaps regression subset selection
LearnBayes Functions for Learning Bayesian Inference
lhs Latin Hypercube Samples
limma Linear Models for Microarray Data
limSolve Solving Linear Inverse Models
linprog Linear Programming / Optimization
listenv Environments Behaving (Almost) as Lists
lme4 Linear Mixed-Effects Models using 'Eigen' and S4
lmomco L-Moments
Lmoments L-Moments and Quantile Mixtures
lmtest Testing Linear Regression Models
locfit Local Regression
longitudinal Analysis of Multiple Time Course Data
loo Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models
LPCM Local Principal Curve Methods
lpridge Local Polynomial (Ridge) Regression
lpSolve Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
lpSolveAPI R Interface to 'lp_solve' Version 5.5.2.0
lsa Latent Semantic Analysis
lsmeans Least-Squares Means
ltm Latent Trait Models under IRT
lubridate Make Dealing with Dates a Little Easier
lumi BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
maanova Tools for analyzing Micro Array experiments
magic create and investigate magic squares
magrittr A Forward-Pipe Operator for R
manipulate Interactive Plots for RStudio
mapdata Extra Map Databases
mapproj Map Projections
maps Draw Geographical Maps
maptools Tools for Reading and Handling Spatial Objects
markdown 'Markdown' Rendering for R
marray Exploratory analysis for two-color spotted microarray data
MARSS Multivariate Autoregressive State-Space Modeling
MASS Support Functions and Datasets for Venables and Ripley's MASS
MatchingFrontier Computation of the Balance - Sample Size Frontier in Matching Methods for Causal Inference
MatchIt MatchIt: Nonparametric Preprocessing for Parametric Casual Inference
matR Metagenomics Analysis Tools for R
Matrix Sparse and Dense Matrix Classes and Methods
matrixcalc Collection of functions for matrix calculations
MatrixEQTL Matrix eQTL: Ultra fast eQTL analysis via large matrix operations
MatrixModels Modelling with Sparse And Dense Matrices
matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors)
MaxentVariableSelection Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling
mboost Model-Based Boosting
mclust Gaussian Mixture Modelling for Model-Based Clustering
mcmc Markov Chain Monte Carlo
MCMCglmm MCMC Generalised Linear Mixed Models
MCMCpack Markov chain Monte Carlo (MCMC) Package
mda Mixture and Flexible Discriminant Analysis
memisc Tools for Management of Survey Data and the Presentation of Analysis Results
memoise Memoisation of Functions
metagenomeSeq Statistical analysis for sparse high-throughput sequencing
methylumi Handle Illumina methylation data
MetStaT Statistical metabolomics tools
MGRASTer API Client for the MG-RAST Server of the US DOE KBase
mi Missing Data Imputation and Model Checking
microbenchmark Accurate Timing Functions
mime Map Filenames to MIME Types
minerva Maximal Information-Based Nonparametric Exploration R Package for Variable Analysis
minfi Analyze Illumina's 450k methylation arrays
minqa Derivative-free optimization algorithms by quadratic approximation
misc3d Miscellaneous 3D Plots
missMethyl Analysis of methylation array data
mitools Tools for multiple imputation of missing data
mixOmics Omics Data Integration Project
mlbench Machine Learning Benchmark Problems
mlegp Maximum Likelihood Estimates of Gaussian Processes
MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers
mmap Map Pages of Memory
mnormt The Multivariate Normal and t Distributions
modeltools Tools and Classes for Statistical Models
mombf Moment and Inverse Moment Bayes Factors
monomvn Estimation for Multivariate Normal and Student-t Data with Monotone Missingness
mpm Multivariate Projection Methods
msdata Various Mass Spectrometry raw data example files
msm Multi-State Markov and Hidden Markov Models in Continuous Time
MTS All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models
multcomp Simultaneous Inference in General Parametric Models
multicool Permutations of Multisets in Cool-Lex Order
multiwayvcov Multi-Way Standard Error Clustering
multtest Resampling-based multiple hypothesis testing
munsell Utilities for Using Munsell Colours
MVA An Introduction to Applied Multivariate Analysis with R
mvtnorm Multivariate Normal and t Distributions
mzR parser for netCDF
NarrowPeaks Shape-based Analysis of Variation in ChIP-seq using Functional PCA
ncbit retrieve and build NBCI taxonomic data
ncdf Interface to Unidata netCDF Data Files
ncvreg Regularization Paths for SCAD and MCP Penalized Regression Models
neldermead R port of the Scilab neldermead module
network Classes for Relational Data
ngspatial Fitting the centered autologistic and sparse spatial generalized linear mixed models for areal data
nleqslv Solve Systems of Nonlinear Equations
nlme Linear and Nonlinear Mixed Effects Models
nloptr R interface to NLopt
NLP Natural Language Processing Infrastructure
nls2 Non-linear regression with brute force
NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS)
NOISeq Exploratory analysis and differential expression for RNA-seq data
nonrandom Stratification and matching by the propensity score
nor1mix Normal (1-d) Mixture Models (S3 Classes and Methods)
numDeriv Accurate Numerical Derivatives
oligo Preprocessing tools for oligonucleotide arrays
oligoClasses Classes for high-throughput arrays supported by oligo and crlmm
openssl Toolkit for Encryption
openxlsx Read
optextras Tools to Support Optimization Methods
optimbase R port of the Scilab optimbase module
optimsimplex R port of the Scilab optimsimplex module
optimx A Replacement and Extension of the optim() Function
optparse Command Line Option Parser
org.Hs.eg.db Genome wide annotation for Human
org.Mm.eg.db Genome wide annotation for Mouse
ouch Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
outliers Tests for outliers
OUwie Analysis of Evolutionary Rates in an OU Framework
packrat A Dependency Management System for Projects and their R Package Dependencies
pamr Pam: prediction analysis for microarrays
ParallelStructure function to run parallel jobs in STRUCTURE
parmigene Parallel Mutual Information estimation for Gene Network reconstruction.
party A Laboratory for Recursive Partytioning
pastis Phylogenetic Assembly with Soft Taxonomic Inferences
pathview a tool set for pathway based data integration and visualization
pbivnorm Vectorized Bivariate Normal CDF
pbkrtest Parametric Bootstrap and Kenward-Roger-Based Methods for Mixed Model Comparison
pcaPP Robust PCA by Projection Pursuit
pd.aragene.1.1.st Platform Design Info for Affymetrix AraGene-1_1-st
pd.huex.1.0.st.v2 Platform Design Info for Affymetrix HuEx-1_0-st-v2
pedigree Pedigree functions
pedigreemm Pedigree-based mixed-effects models
peer PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.
perm Exact or Asymptotic permutation tests
permute Functions for Generating Restricted Permutations of Data
phangorn Phylogenetic Analysis in R
pheatmap Pretty Heatmaps
phia Post-Hoc Interaction Analysis
phybase Basic functions for phylogenetic analysis
phyext An extension of some of the classes in phylobase. Tree objects now support subnodes on branches
phylobase Base Package for Phylogenetic Structures and Comparative Data
phyloseq Handling and analysis of high-throughput microbiome census data
phytools Phylogenetic Tools for Comparative Biology (and Other Things)
picante R tools for integrating phylogenies and ecology
pixmap Bitmap Images (``Pixel Maps)
pkgmaker Package development utilities
PKI Public Key Infrastucture for R Based on the X.509 Standard
plier Implements the Affymetrix PLIER algorithm
plotrix Various Plotting Functions
pls Partial Least Squares and Principal Component Regression
plyr Tools for Splitting
png Read and write PNG images
polspline Polynomial Spline Routines
polyclip Polygon Clipping
polycor Polychoric and Polyserial Correlations
pomp Statistical Inference for Partially Observed Markov Processes
PopGenome An Efficient Swiss Army Knife for Population Genomic Analyses
prabclus Functions for Clustering of Presence-Absence
praise Praise Users
preprocessCore A collection of pre-processing functions
prettyR Pretty Descriptive Stats
pROC Display and Analyze ROC Curves
PROcess Ciphergen SELDI-TOF Processing
proftools Profile Output Processing Tools for R
proj4 A simple interface to the PROJ.4 cartographic projections library
ProtGenerics S4 generic functions for Bioconductor proteomics infrastructure
proto Prototype object-based programming
pryr Tools for Computing on the Language
PSCBS Analysis of Parent-Specific DNA Copy Numbers
pscl Political Science Computational Laboratory
psiplot Generate plots of PSI values generated by vast-tools
psych Procedures for Psychological
ptw Parametric Time Warping
pvclust Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling
qgraph Graph Plotting Methods
qqman Q-Q and manhattan plots for GWAS data
qtl Tools for Analyzing QTL Experiments
quadprog Functions to solve Quadratic Programming Problems.
quantreg Quantile Regression
qvalue Q-value estimation for false discovery rate control
R2admb 'ADMB' to R Interface Functions
R2jags Using R to Run 'JAGS'
R2WinBUGS Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'
R6 Classes with Reference Semantics
RandomFields Simulation and Analysis of Random Fields
RandomFieldsUtils Utilities for the Simulation and Analysis of Random Fields
randomForest Breiman and Cutler's Random Forests for Classification and Regression
randomForestSRC Random Forests for Survival
RankProd Rank Product method for identifying differentially expressed genes with application in meta-analysis
raster Geographic Data Analysis and Modeling
rasterVis Visualization Methods for Raster Data
RBGL An interface to the BOOST graph library
R.cache Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
Rcgmin Conjugate Gradient Minimization of Nonlinear Functions
Rcmdr R Commander
RcmdrMisc R Commander Miscellaneous Functions
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
RcppParallel Parallel Programming Tools for 'Rcpp'
RCurl General Network (HTTP/FTP/...) Client Interface for R
rda Shrunken Centroids Regularized Discriminant Analysis
R.devices Unified Handling of Graphics Devices
readr Read Tabular Data
readstata13 Import Stata Data Files
readxl Read Excel Files
registry Infrastructure for R Package Registries
relaimpo Relative importance of regressors in linear models
relimp Relative Contribution of Effects in a Regression Model
rentrez Entrez in R
RepeatABEL GWAS for Multiple Observations on Related Individuals
reshape Flexibly reshape data.
reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package.
rexpokit R wrappers for EXPOKIT; other matrix functions
R.filesets Easy Handling of and Access to Files Organized in Structured Directories
rgdal Bindings for the Geospatial Data Abstraction Library
rgenoud R Version of GENetic Optimization Using Derivatives
rgeos Interface to Geometry Engine - Open Source (GEOS)
rgl 3D Visualization Using OpenGL
RgoogleMaps Overlays on Google map tiles in R
Rgraphviz Provides plotting capabilities for R graph objects
RGtk2 R bindings for Gtk 2.8.0 and above
R.huge Methods for Accessing Huge Amounts of Data [deprecated]
ridigbio Interface to the iDigBio Data API
Ringo R Investigation of ChIP-chip Oligoarrays
rjags Bayesian Graphical Models using MCMC
rJava Low-Level R to Java Interface
rjson JSON for R
RJSONIO Serialize R objects to JSON
Rlab Functions and Datasets Required for ST370 class
RMark R Code for Mark Analysis
rmarkdown Dynamic Documents for R
R.matlab Read and Write MAT Files and Call MATLAB from Within R
R.methodsS3 S3 Methods Simplified
RmiR.hsa Various databases of microRNA Targets
Rmisc Rmisc: Ryan Miscellaneous
Rmpfr R MPFR - Multiple Precision Floating-Point Reliable
rms Regression Modeling Strategies
RMySQL Database Interface and 'MySQL' Driver for R
rncl An Interface to the Nexus Class Library
RNetCDF R Interface to NetCDF Datasets
RNeXML Semantically Rich I/O for the 'NeXML' Format
rngtools Utility functions for working with Random Number Generators
robustbase Basic Robust Statistics
ROC utilities for ROC
ROCR Visualizing the Performance of Scoring Classifiers
R.oo R Object-Oriented Programming with or without References
rootSolve Nonlinear Root Finding
roxygen2 In-Source Documentation for R
rpanel Simple interactive controls for R using the tcltk library.
RPMM Recursively Partitioned Mixture Model
rrBLUP Ridge Regression and Other Kernels for Genomic Selection
rrcov Scalable Robust Estimators with High Breakdown Point
R.rsp Dynamic Generation of Scientific Reports
Rsamtools Binary alignment (BAM)
rsconnect Deployment Interface for R Markdown Documents and Shiny Applications
Rserve Binary R server
rsgcc Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data
Rsolnp General Non-Linear Optimization
RSQLite SQLite Interface for R
RSQLite.extfuns Math and String Extension Functions for RSQLite
Rssa A Collection of Methods for Singular Spectrum Analysis
rstan R Interface to Stan
rstudio Tools and Utilities for RStudio
rstudioapi Safely Access the RStudio API
Rsubread Subread sequence alignment for R
rtracklayer R interface to genome browsers and their annotation tracks
RUnit R Unit Test Framework
R.utils Various Programming Utilities
ruv Detect and Remove Unwanted Variation using Negative Controls
RUVSeq Remove Unwanted Variation from RNA-Seq Data
rversions Query 'R' Versions
rvest Easily Harvest (Scrape) Web Pages
Rvmmin Variable Metric Nonlinear Function Minimization
Rwave Time-Frequency Analysis of 1-D Signals
RWeka R/Weka interface
RWekajars R/Weka interface jars
S4Vectors S4 implementation of vectors and lists
sandwich Robust Covariance Matrix Estimators
scales Scale Functions for Visualization
scatterplot3d 3D Scatter Plot
scDD Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
sealasso Standard Error Adjusted Adaptive Lasso
season Seasonal analysis of health data
segmented Regression Models with Breakpoints/Changepoints Estimation
selectr Translate CSS Selectors to XPath Expressions
sem Structural Equation Models
SemiPar Semiparametic Regression
seqinr Biological Sequences Retrieval and Analysis
seqLogo Sequence logos for DNA sequence alignments
seqMeta Meta-Analysis of Region-Based Tests of Rare DNA Variants
setRNG Set (Normal) Random Number Generator and Seed
sfsmisc Utilities from "Seminar fuer Statistik" ETH Zurich
SGL Fit a GLM (or cox model) with a combination of lasso and group lasso regularization
shapefiles Read and Write ESRI Shapefiles
shiny Web Application Framework for R
shinydashboard Create Dashboards with 'Shiny'
shinyjs Perform Common JavaScript Operations in Shiny Apps using Plain R Code
shinystan Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
shinythemes Themes for Shiny
ShortRead FASTQ input and manipulation
siggenes Multiple testing using SAM and Efron's empirical Bayes approaches
simpleaffy Very simple high level analysis of Affymetrix data
SimRAD Simulations to Predict the Number of RAD and GBS Loci
simsem SIMulated Structural Equation Modeling
slam Sparse Lightweight Arrays and Matrices
sna Tools for Social Network Analysis
snow Simple Network of Workstations
SnowballC Snowball stemmers based on the C libstemmer UTF-8 library
snowfall Easier cluster computing (based on snow).
SNPassoc SNPs-based whole genome association studies
SNPchip Visualizations for copy number alterations
SNPRelate Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data
sp Classes and Methods for Spatial Data
spacetime Classes and Methods for Spatio-Temporal Data
spam SPArse Matrix
SparseM Sparse Linear Algebra
spatial.tools R functions for working with spatial data.
SpatioTemporal Spatio-Temporal Model Estimation
spatstat Spatial Point Pattern Analysis
spBayes Univariate and Multivariate Spatial-temporal Modeling
spdep Spatial Dependence: Weighting Schemes
SPEI Calculation of the Standardised Precipitation-Evapotranspiration Index
spgwr Geographically Weighted Regression
splancs Spatial and Space-Time Point Pattern Analysis
spTDyn Spatially Varying and Spatio-Temporal Dynamic Linear Models
sqldf Perform SQL Selects on R Data Frames
stabledist Stable Distribution Functions
stabs Stability Selection with Error Control
StanHeaders C++ Header Files for Stan
stargazer Well-Formatted Regression and Summary Statistics Tables
statmod Statistical Modeling
STITCH STITCH - Sequencing To Imputation Through Constructing Haplotypes
stringi Character String Processing Facilities
stringr Simple
strucchange Testing
subplex Unconstrained Optimization using the Subplex Algorithm
SummarizedExperiment SummarizedExperiment container
SuppDists Supplementary Distributions
survey analysis of complex survey samples
survival Survival Analysis
sva Surrogate Variable Analysis
svd Interfaces to Various State-of-Art SVD and Eigensolvers
SVGAnnotation Tools for post-processing SVG plots created in R
svUnit SciViews GUI API - Unit testing
tau Text Analysis Utilities
taxize Taxonomic Information from Around the Web
tcltk2 Tcl/Tk Additions
tensor Tensor product of arrays
tensorA Advanced tensors arithmetic with named indices
testthat Unit Testing for R
tfplot Time Frame User Utilities
tframe Time Frame Coding Kernel
TH.data TH's Data Archive
threejs Interactive 3D Scatter Plots
tibble Simple Data Frames
tidyr Easily Tidy Data with `spread()` and `gather()` Functions
tilingArray Transcript mapping with high-density oligonucleotide tiling arrays
timeDate Rmetrics - Chronological and Calendar Objects
timeSeries Rmetrics - Financial Time Series Objects
tm Text Mining Package
tmvtnorm Truncated Multivariate Normal and Student t Distribution
topGO topGO: Enrichment analysis for Gene Ontology
TreeSim Simulating Phylogenetic Trees
trimcluster Cluster analysis with trimming
truncnorm Truncated normal distribution
trust Trust Region Optimization
TSA Time Series Analysis
tseries Time Series Analysis and Computational Finance
tseriesChaos Analysis of nonlinear time series
tviz Visualisation of gene and transcript expression levels from RNA-seq experiments
TxDb.Hsapiens.UCSC.hg19.knownGene Annotation package for TxDb object(s)
ucminf General-purpose unconstrained non-linear optimization
unmarked Models for Data from Unmarked Animals
urca Unit Root and Cointegration Tests for Time Series Data
usdm Uncertainty Analysis for Species Distribution Models
uuid Tools for generating and handling of UUIDs
VariantAnnotation Annotation of Genetic Variants
vars VAR Modelling
varSelectIP Objective Bayes Model Selection
varSelRF Variable Selection using Random Forests
vcd Visualizing Categorical Data
vegan Community Ecology Package
VennDiagram Generate High-Resolution Venn and Euler Plots
VGAM Vector Generalized Linear and Additive Models
viridisLite Default Color Maps from 'matplotlib' (Lite Version)
visNetwork Network Visualization using 'vis.js' Library
vsn Variance stabilization and calibration for microarray data
wateRmelon Illumina 450 methylation array normalization and metrics
wavelets A package of functions for computing wavelet filters
waveslim Basic wavelet routines for one-
wavethresh Wavelets statistics and transforms.
WGCNA Weighted Correlation Network Analysis
WGDgc Whole genome duplication detection using gene counts
whisker {{mustache}} for R
withr Run Code 'With' Temporarily Modified Global State
wordcloud Word Clouds
xcms LC/MS and GC/MS Data Analysis
xlsx Read
xlsxjars Package required POI jars for the xlsx package
XML Tools for Parsing and Generating XML Within R and S-Plus
xml2 Parse XML
xpose4 Tools for Nonlinear Mixed-Effect Model Building and Diagnostics
xps Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays
xtable Export Tables to LaTeX or HTML
xts eXtensible Time Series
XVector Representation and manpulation of external sequences
yaml Methods to convert R data to YAML and back
zlibbioc An R packaged zlib-1.2.5
zoo S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)
base The R Base Package
boot Bootstrap Functions (Originally by Angelo Canty for S)
class Functions for Classification
cluster Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al.
codetools Code Analysis Tools for R
compiler The R Compiler Package
datasets The R Datasets Package
foreign Read Data Stored by Minitab
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours and Fonts
grid The Grid Graphics Package
KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995)
lattice Trellis Graphics for R
MASS Support Functions and Datasets for Venables and Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
methods Formal Methods and Classes
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation
nlme Linear and Nonlinear Mixed Effects Models
nnet Feed-Forward Neural Networks and Multinomial Log-Linear Models
parallel Support for Parallel computation in R
rpart Recursive Partitioning and Regression Trees
spatial Functions for Kriging and Point Pattern Analysis
splines Regression Spline Functions and Classes
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
survival Survival Analysis
tcltk Tcl/Tk Interface
tools Tools for Package Development
utils The R Utils Package