R

Description
R is a free software environment for statistical computing and graphics.
Note: File a support ticket to request installation of additional libraries.
Required Modules
Serial
 R
 HPC_R_BIN  executable directory
 HPC_R_LIB  library directory
 HPC_R_INCLUDE  includes directory
To use the version of R built for parallel execution with MPI via the Rmpi library load the following modules:
module load intel/11.1 openmpi/1.4.3 R
Installed Libraries
Note: Many of the packages in the R library shown below are installed as a part of Bioconductor metalibrary. The list is generated from the default R version.
Name  Description 

a4Core  Automated Affymetrix Array Analysis Core Package 
a4Preproc  Automated Affymetrix Array Analysis Preprocessing Package 
abind  Combine Multidimensional Arrays 
acepack  ACE and AVAS for Selecting Multiple Regression Transformations 
adabag  Applies Multiclass AdaBoost.M1 
adagio  Discrete and Global Optimization Routines 
ade4  Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences 
adegenet  Exploratory Analysis of Genetic and Genomic Data 
AdhereR  Adherence to Medications 
adnuts  NoUTurn MCMC Sampling for 'ADMB' and 'TMB' Models 
affxparser  Affymetrix File Parsing SDK 
affy  Methods for Affymetrix Oligonucleotide Arrays 
affyio  Tools for parsing Affymetrix data files 
affyPLM  Methods for fitting probelevel models 
AGHmatrix  Relationship matrices for diploid and autopolyploid species 
agricolae  Statistical Procedures for Agricultural Research 
akima  Interpolation of Irregularly and Regularly Spaced Data 
ALDEx2  Analysis Of Differential Abundance Taking Sample Variation Into Account 
AlgDesign  Algorithmic Experimental Design 
amap  Another Multidimensional Analysis Package 
Amelia  A Program for Missing Data 
animation  A Gallery of Animations in Statistics and Utilities to Create Animations 
annaffy  Annotation tools for Affymetrix biological metadata 
annotate  Annotation for microarrays 
AnnotationDbi  Annotation Database Interface 
AnnotationFilter  Facilities for Filtering Bioconductor Annotation Resources 
AnnotationHub  Client to access AnnotationHub resources 
annotSnpStats  Annotated SnpMatrix objects 
apcluster  Affinity Propagation Clustering 
ape  Analyses of Phylogenetics and Evolution 
arm  Data Analysis Using Regression and Multilevel/Hierarchical Models 
aroma.light  LightWeight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types 
arrayQualityMetrics  Quality metrics report for microarray data sets 
assertive  Readable Check Functions to Ensure Code Integrity 
assertive.base  A Lightweight Core of the 'assertive' Package 
assertive.code  Assertions to Check Properties of Code 
assertive.data  Assertions to Check Properties of Data 
assertive.data.uk  Assertions to Check Properties of Strings 
assertive.data.us  Assertions to Check Properties of Strings 
assertive.datetimes  Assertions to Check Properties of Dates and Times 
assertive.files  Assertions to Check Properties of Files 
assertive.matrices  Assertions to Check Properties of Matrices 
assertive.models  Assertions to Check Properties of Models 
assertive.numbers  Assertions to Check Properties of Numbers 
assertive.properties  Assertions to Check Properties of Variables 
assertive.reflection  Assertions for Checking the State of R 
assertive.sets  Assertions to Check Properties of Sets 
assertive.strings  Assertions to Check Properties of Strings 
assertive.types  Assertions to Check Types of Variables 
assertthat  Easy Pre and Post Assertions 
automap  Automatic interpolation package 
backports  Reimplementations of Functions Introduced Since R3.0.0 
ballgown  Flexible 
BAMMtools  Analysis and Visualization of Macroevolutionary Dynamics on Phylogenetic Trees 
base64  Base64 Encoder and Decoder 
base64enc  Tools for base64 encoding 
baseline  Baseline Correction of Spectra 
bayesm  Bayesian Inference for Marketing/MicroEconometrics 
bayesplot  Plotting for Bayesian Models 
bazar  Miscellaneous Basic Functions 
BB  Solving and Optimizing LargeScale Nonlinear Systems 
bbmle  Tools for General Maximum Likelihood Estimation 
bdsmatrix  Routines for Block Diagonal Symmetric Matrices 
beadarray  Quality assessment and lowlevel analysis for Illumina BeadArray data 
BeadDataPackR  Compression of Illumina BeadArray data 
beanplot  Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot) 
BEDMatrix  Extract Genotypes from a PLINK .bed File 
bestglm  Best Subset GLM and Regression Utilities 
BGData  A Suite of Packages for Analysis of Big Genomic Data 
BGLR  Bayesian Generalized Linear Regression 
BH  Boost C++ Header Files 
BiasedUrn  Biased Urn Model Distributions 
bibtex  Bibtex Parser 
biganalytics  Utilities for 'big.matrix' Objects from Package 'bigmemory' 
big.char  Provides Very Large Vectors of Character Strings 
big.data.frame  Extend big.char and bigmemory's big.matrix to support largerthanRAM data.framelike objects in R. 
biglm  bounded memory linear and generalized linear models 
bigmemory  Manage Massive Matrices with Shared Memory and MemoryMapped Files 
bigmemory.sri  A shared resource interface for Bigmemory Project packages 
BigVAR  Dimension Reduction Methods for Multivariate Time Series 
bindr  Parametrized Active Bindings 
bindrcpp  An 'Rcpp' Interface to Active Bindings 
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 
biomaRt  Interface to BioMart databases (e.g. Ensembl 
biomformat  An interface package for the BIOM file format 
Biostrings  Efficient manipulation of biological strings 
biovizBase  Basic graphic utilities for visualization of genomic data. 
bipartite  Visualising Bipartite Networks and Calculating Some (Ecological) Indices 
bit  A Class for Vectors of 1Bit Booleans 
bit64  A S3 Class for Vectors of 64bit Integers 
bitops  Bitwise Operations 
blob  A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS') 
blockmodeling  Generalized and Classical Blockmodeling of Valued Networks 
bold  Interface to Bold Systems API 
Boom  Bayesian Object Oriented Modeling 
BoomSpikeSlab  MCMC for Spike and Slab Regression 
boot  Bootstrap Functions (Originally by Angelo Canty for S) 
brew  Templating Framework for Report Generation 
broom  Convert Statistical Analysis Objects into Tidy Data Frames 
BSgenome  Software infrastructure for efficient representation of full genomes and their SNPs 
BSgenome.Hsapiens.UCSC.hg19  Full genome sequences for Homo sapiens (UCSC version hg19) 
bsts  Bayesian Structural Time Series 
bumphunter  Bump Hunter 
BurStFin  Burns Statistics Financial 
Cairo  R graphics device using cairo graphics library for creating highquality bitmap (PNG 
calibrate  Calibration of Scatterplot and Biplot Axes 
callr  Call R from R 
CAMERA  Collection of annotation related methods for mass spectrometry data 
car  Companion to Applied Regression 
carData  Companion to Applied Regression Data Sets 
caret  Classification and Regression Training 
caTools  Tools: moving window statistics 
CCA  Canonical correlation analysis 
cccrm  Concordance Correlation Coefficient for Repeated (and NonRepeated) Measures 
ccdrAlgorithm  CCDr Algorithm for Learning Sparse Gaussian Bayesian Networks 
cellranger  Translate Spreadsheet Cell Ranges to Rows and Columns 
checkmate  Fast and Versatile Argument Checks 
ChemoSpec  Exploratory Chemometrics for Spectroscopy 
chopsticks  The snp.matrix and X.snp.matrix classes 
chron  Chronological Objects which can Handle Dates and Times 
circlize  Circular Visualization 
cladoRcpp  C++ implementations of phylogenetic cladogenesis calculations 
class  Functions for Classification 
classInt  Choose Univariate Class Intervals 
cleangeo  Cleaning Geometries from Spatial Objects 
cli  Helpers for Developing Command Line Interfaces 
clipr  Read and Write from the System Clipboard 
clue  Cluster Ensembles 
cluster  Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al. 
clusterGeneration  Random Cluster Generation (with Specified Degree of Separation) 
clusterProfiler  statistical analysis and visualization of functional profiles for genes and gene clusters 
cnv  Detection of Copy Number Variation by Sequencing 
coda  Output Analysis and Diagnostics for MCMC 
codetools  Code Analysis Tools for R 
coin  Conditional Inference Procedures in a Permutation Test Framework 
colorspace  Color Space Manipulation 
colourpicker  A Colour Picker Tool for Shiny and for Selecting Colours in Plots 
combinat  combinatorics utilities 
commonmark  High Performance CommonMark and Github Markdown Rendering in R 
compare  Comparing Objects for Differences 
ComplexHeatmap  Making Complex Heatmaps 
compositions  Compositional Data Analysis 
CompRandFld  CompositeLikelihood Based Analysis of Random Fields 
concaveman  A Very Fast 2D Concave Hull Algorithm 
CondReg  Condition Number Regularized Covariance Estimation 
config  Manage Environment Specific Configuration Values 
corpcor  Efficient Estimation of Covariance and (Partial) Correlation 
covr  Test Coverage for Packages 
cowplot  Streamlined Plot Theme and Plot Annotations for 'ggplot2' 
CpGassoc  Association Between Methylation and a Phenotype of Interest 
crayon  Colored Terminal Output 
crch  Censored Regression with Conditional Heteroscedasticity 
crmn  CCMN and other noRMalizatioN methods for metabolomics data 
crochet  Implementation Helper for [ and [< Of Custom MatrixLike Types 
crosstalk  InterWidget Interactivity for HTML Widgets 
crul  HTTP Client 
cubature  Adaptive Multivariate Integration over Hypercubes 
curl  A Modern and Flexible Web Client for R 
CVST  Fast CrossValidation via Sequential Testing 
cvTools  Crossvalidation tools for regression models 
dagitty  Graphical Analysis of Structural Causal Models 
DASTool  DAS Tool  Dereplication Aggregation and Scoring Tool for genomeresolved metagenomics 
DatABEL  FileBased Access to Large Matrices Stored on HDD in Binary Format 
data.table  Extension of `data.frame` 
date  Functions for Handling Dates 
DBI  R Database Interface 
dbplyr  A 'dplyr' Back End for Databases 
dcurver  Utility Functions for Davidian Curves 
ddalpha  DepthBased Classification and Calculation of Data Depth 
debugme  Debug R Packages 
DelayedArray  Delayed operations on arraylike objects 
deldir  Delaunay Triangulation and Dirichlet (Voronoi) Tessellation 
denstrip  Density Strips and Other Methods for Compactly Illustrating Distributions 
DEoptimR  Differential Evolution Optimization in Pure R 
depmixS4  Dependent Mixture Models  Hidden Markov Models of GLMs and Other Distributions in S4 
Deriv  Symbolic Differentiation 
desc  Manipulate DESCRIPTION Files 
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 
dfoptim  DerivativeFree Optimization 
dichromat  Color Schemes for Dichromats 
diffusionMap  Diffusion map 
digest  Create Compact Hash Digests of R Objects 
dimRed  A Framework for Dimensionality Reduction 
diptest  Hartigan's Dip Test Statistic for Unimodality  Corrected 
discretecdAlgorithm  CoordinateDescent Algorithm for Learning Sparse Discrete Bayesian Networks 
dismo  Species Distribution Modeling 
diversitree  Comparative 'Phylogenetic' Analyses of Diversification 
dlm  Bayesian and Likelihood Analysis of Dynamic Linear Models 
doBy  Groupwise Statistics 
DO.db  A set of annotation maps describing the entire Disease Ontology 
doMC  Foreach Parallel Adaptor for 'parallel' 
doParallel  Foreach Parallel Adaptor for the 'parallel' Package 
doRNG  Generic Reproducible Parallel Backend for 'foreach' Loops 
DOSE  Disease Ontology Semantic and Enrichment analysis 
doSNOW  Foreach Parallel Adaptor for the 'snow' Package 
dotCall64  Enhanced Foreign Function Interface Supporting Long Vectors 
dplyr  A Grammar of Data Manipulation 
DRR  Dimensionality Reduction via Regression 
DT  A Wrapper of the JavaScript Library 'DataTables' 
dtw  Dynamic Time Warping Algorithms 
dupRadar  Assessment of duplication rates in RNASeq datasets 
dygraphs  Interface to 'Dygraphs' Interactive Time Series Charting Library 
dynamicTreeCut  Methods for Detection of Clusters in Hierarchical Clustering Dendrograms 
e1071  Misc Functions of the Department of Statistics 
earth  Multivariate Adaptive Regression Splines 
EbayesThresh  Empirical Bayes Thresholding and Related Methods 
EBImage  Image processing and analysis toolbox for R 
EBSeq  An R package for gene and isoform differential expression analysis of RNAseq data 
edgeR  Empirical Analysis of Digital Gene Expression Data in R 
eDNAoccupancy  Multiscale Occupancy Modeling of Environmental DNA Data 
egg  Extensions for 'ggplot2': Custom Geom 
ellipse  Functions for Drawing Ellipses and EllipseLike Confidence Regions 
emdbook  Support Functions and Data for "Ecological Models and Data" 
emulator  Bayesian Emulation of Computer Programs 
energy  EStatistics: Multivariate Inference via the Energy of Data 
EnsDb.Hsapiens.v75  Ensembl based annotation package 
ensembldb  Utilities to create and use Ensemblbased annotation databases 
equateIRT  IRT Equating Methods 
estimability  Tools for Assessing Estimability of Linear Predictions 
EthSEQ  Ethnicity Annotation from Whole Exome Sequencing Data 
evaluate  Parsing and Evaluation Tools that Provide More Details than the Default 
evd  Functions for Extreme Value Distributions 
expm  Matrix Exponential 
fastAdaboost  a Fast Implementation of Adaboost 
fastcluster  Fast Hierarchical Clustering Routines for R and 'Python' 
fastICA  FastICA Algorithms to Perform ICA and Projection Pursuit 
fastmatch  Fast match() function 
fastseg  fastseg  a fast segmentation algorithm 
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 
fdth  Frequency Distribution Tables 
ff  MemoryEfficient Storage of Large Data on Disk and Fast Access Functions 
fftwtools  Wrapper for 'FFTW3' Includes: OneDimensional Univariate 
fGarch  Rmetrics  Autoregressive Conditional Heteroskedastic Modelling 
FGN  Fractional Gaussian Noise and power law decay time series model fitting 
fgsea  Fast Gene Set Enrichment Analysis 
fields  Tools for Spatial Data 
FinTS  Companion to Tsay (2005) Analysis of Financial Time Series 
fitdistrplus  Help to Fit of a Parametric Distribution to NonCensored or Censored Data 
fit.models  Compare Fitted Models 
flare  Family of Lasso Regression 
flexmix  Flexible Mixture Modeling 
FNN  Fast Nearest Neighbor Search Algorithms and Applications 
forcats  Tools for Working with Categorical Variables (Factors) 
foreach  Provides Foreach Looping Construct for R 
forecast  Forecasting Functions for Time Series and Linear Models 
foreign  Read Data Stored by 'Minitab' 
formatR  Format R Code Automatically 
Formula  Extended Model Formulas 
fpc  Flexible Procedures for Clustering 
fracdiff  Fractionally differenced ARIMA aka ARFIMA(p 
fst  Lightning Fast Serialization of Data Frames for R 
futile.logger  A Logging Utility for R 
futile.matrix  Random Matrix Generation and Manipulation 
futile.options  Futile Options Management 
future  Unified Parallel and Distributed Processing in R for Everyone 
future.apply  Apply Function to Elements in Parallel using Futures 
GA  Genetic Algorithms 
GAabbreviate  Abbreviating Items Measures using Genetic Algorithms 
gap  Genetic Analysis Package 
gapminder  Data from Gapminder 
gbm  Generalized Boosted Regression Models 
gcrma  Background Adjustment Using Sequence Information 
gdalUtils  Wrappers for the Geospatial Data Abstraction Library (GDAL) Utilities 
gdata  Various R Programming Tools for Data Manipulation 
gdmp  Genomic Data Management 
gdsfmt  R Interface to CoreArray Genomic Data Structure (GDS) Files 
gdtools  Utilities for Graphical Rendering 
geeM  Solve Generalized Estimating Equations 
geepack  Generalized Estimating Equation Package 
geigen  Calculate Generalized Eigenvalues 
geiger  Analysis of Evolutionary Diversification 
GenABEL  genomewide SNP association analysis 
GenABEL.data  Package contains data which is used by GenABEL example and test functions 
gender  Predict Gender from Names Using Historical Data 
genefilter  genefilter: methods for filtering genes from highthroughput experiments 
geneplotter  Graphics related functions for Bioconductor 
GeneSelector  Stability and Aggregation of ranked gene lists 
genetics  Population Genetics 
genlasso  Path algorithm for generalized lasso problems 
GenomeInfoDb  Utilities for manipulating chromosome and other 'seqname' identifiers 
GenomeInfoDbData  Species and taxonomy ID look up tables used by GenomeInfoDb 
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 
geometry  Mesh Generation and Surface Tesselation 
GEOquery  Get data from NCBI Gene Expression Omnibus (GEO) 
geosphere  Spherical Trigonometry 
getopt  CLike 'getopt' Behavior 
GetoptLong  Parsing CommandLine Arguments and Variable Interpolation 
GGally  Extension to 'ggplot2' 
ggbio  Visualization tools for genomic data 
ggdendro  Create Dendrograms and Tree Diagrams Using 'ggplot2' 
ggjoy  Joyplots in 'ggplot2' 
ggm  Functions for graphical Markov models 
ggplot2  Create Elegant Data Visualisations Using the Grammar of Graphics 
ggplot2movies  Movies Data 
ggpubr  'ggplot2' Based Publication Ready Plots 
ggRandomForests  Visually Exploring Random Forests 
ggrepel  Automatically Position NonOverlapping Text Labels with 'ggplot2' 
ggridges  Ridgeline Plots in 'ggplot2' 
ggsci  Scientific Journal and SciFi Themed Color Palettes for 'ggplot2' 
ggsignif  Significance Brackets for 'ggplot2' 
ggtree  an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data 
ggvis  Interactive Grammar of Graphics 
GIGrvg  Random Variate Generator for the GIG Distribution 
git2r  Provides Access to Git Repositories 
glasso  Graphical lasso estimation of Gaussian graphical models 
glm2  Fitting Generalized Linear Models 
glmmLasso  Variable Selection for Generalized Linear Mixed Models by L1Penalized Estimation 
glmnet  Lasso and ElasticNet Regularized Generalized Linear Models 
GlobalOptions  Generate Functions to Get or Set Global Options 
globals  Identify Global Objects in R Expressions 
glue  Interpreted String Literals 
gmailr  Access the Gmail RESTful API 
gmodels  Various R Programming Tools for Model Fitting 
gmp  Multiple Precision Arithmetic 
GO.db  A set of annotation maps describing the entire Gene Ontology 
GOSemSim  GOterms Semantic Similarity Measures 
gower  Gower's Distance 
GPArotation  GPA Factor Rotation 
gplots  Various R Programming Tools for Plotting Data 
graph  graph: A package to handle graph data structures 
gridBase  Integration of base and grid graphics 
gridExtra  Miscellaneous Functions for "Grid" Graphics 
gridSVG  Export 'grid' Graphics as SVG 
grplasso  Fitting user specified models with Group Lasso penalty 
grpreg  Regularization Paths for Regression Models with Grouped Covariates 
gss  General Smoothing Splines 
gstat  Spatial and SpatioTemporal Geostatistical Modelling 
gsubfn  Utilities for Strings and Function Arguments 
gtable  Arrange 'Grobs' in Tables 
gtools  Various R Programming Tools 
GUESSFM  Using GUESS for Fine Mapping 
hashmap  The Faster Hash Map 
haven  Import and Export 'SPSS' 
hdf5r  Interface to the 'HDF5' Binary Data Format 
HDMD  Statistical Analysis Tools for High Dimension Molecular Data (HDMD) 
hexbin  Hexagonal Binning Routines 
highr  Syntax Highlighting for R Source Code 
HKprocess  HurstKolmogorov Process 
Hmisc  Harrell Miscellaneous 
hms  Pretty Time of Day 
horseshoe  Implementation of the Horseshoe Prior 
hpar  Human Protein Atlas in R 
htmlTable  Advanced Tables for Markdown/HTML 
htmltools  Tools for HTML 
htmlwidgets  HTML Widgets for R 
httpcode  'HTTP' Status Code Helper 
httpuv  HTTP and WebSocket Server Library 
httr  Tools for Working with URLs and HTTP 
huge  HighDimensional Undirected Graph Estimation 
hunspell  HighPerformance Stemmer 
hwriter  HTML Writer  Outputs R objects in HTML format 
hydroGOF  GoodnessofFit Functions for Comparison of Simulated and Observed Hydrological Time Series 
hydroTSM  Time Series Management 
hyperSpec  Work with Hyperspectral Data 
ica  Independent Component Analysis 
igraph  Network Analysis and Visualization 
illuminaio  Parsing Illumina Microarray Output Files 
impute  impute: Imputation for microarray data 
indicspecies  Relationship Between Species and Groups of Sites 
inline  Functions to Inline C 
intansv  Integrative analysis of structural variations 
interactiveDisplayBase  Base package for enabling powerful shiny web displays of Bioconductor objects 
intervals  Tools for Working with Points and Intervals 
IONiseR  Quality Assessment Tools for Oxford Nanopore MinION data 
IPO  Automated Optimization of XCMS Data Processing parameters 
ipred  Improved Predictors 
ipw  Estimate Inverse Probability Weights 
IRanges  Infrastructure for manipulating intervals on sequences 
IRdisplay  'Jupyter' Display Machinery 
IRkernel  Native R Kernel for the 'Jupyter Notebook' 
irlba  Fast Truncated Singular Value Decomposition and Principal Components Analysis for Large Dense and Sparse Matrices 
itcSegment  Individual Tree Crowns Segmentation 
iterators  Provides Iterator Construct for R 
itertools  Iterator Tools 
jagsUI  A Wrapper Around 'rjags' to Streamline 'JAGS' Analyses 
jomo  Multilevel Joint Modelling Multiple Imputation 
jpeg  Read and write JPEG images 
jsonlite  A Robust 
kebabs  KernelBased Analysis Of Biological Sequences 
KEGG.db  A set of annotation maps for KEGG 
KEGGgraph  KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor 
KEGGprofile  An annotation and visualization package for multitypes and multigroups expression data in KEGG pathway 
KEGGREST  Clientside REST access to KEGG 
keras  R Interface to 'Keras' 
kerasR  R Interface to the Keras Deep Learning Library 
kernlab  KernelBased Machine Learning Lab 
KernSmooth  Functions for Kernel Smoothing Supporting Wand & Jones (1995) 
KFAS  Kalman Filter and Smoother for Exponential Family State Space Models 
kimisc  Kirill's Miscellaneous Functions 
kinship2  Pedigree Functions 
klaR  Classification and Visualization 
knitr  A GeneralPurpose Package for Dynamic Report Generation in R 
labeling  Axis Labeling 
labelled  Manipulating Labelled Data 
lambda.r  Modeling Data with Functional Programming 
lambda.tools  Tools for Modeling Data with Functional Programming 
lars  Least Angle Regression 
lassoshooting  L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting 
later  Utilities for Delaying Function Execution 
lattice  Trellis Graphics for R 
latticeExtra  Extra Graphical Utilities Based on Lattice 
lava  Latent Variable Models 
lavaan  Latent Variable Analysis 
lavaan.survey  Complex Survey Structural Equation Modeling (SEM) 
lazyeval  Lazy (NonStandard) Evaluation 
LDcorSV  Linkage Disequilibrium Corrected by the Structure and the Relatedness 
LDheatmap  Graphical Display of Pairwise Linkage Disequilibria Between SNPs 
leaflet  Create Interactive Web Maps with the JavaScript 'Leaflet' Library 
leaflet.extras  Extra Functionality for 'leaflet' Package 
leaps  Regression Subset Selection 
LearnBayes  Functions for Learning Bayesian Inference 
lfmm  Latent Factor Mixed Models 
LiblineaR  Linear Predictive Models Based on the 'LIBLINEAR' C/C++ Library 
lidR  Airborne LiDAR Data Manipulation and Visualization for Forestry Applications 
limma  Linear Models for Microarray Data 
limSolve  Solving Linear Inverse Models 
LinkedMatrix  ColumnLinked and RowLinked Matrices 
lintr  A 'Linter' for R Code 
listenv  Environments Behaving (Almost) as Lists 
lme4  Linear MixedEffects Models using 'Eigen' and S4 
lmmen  Linear Mixed Model Elastic Net 
lmmlasso  Linear mixedeffects models with Lasso 
lmtest  Testing Linear Regression Models 
locfit  Local Regression 
loo  Efficient LeaveOneOut CrossValidation and WAIC for Bayesian Models 
lpSolve  Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs 
lsgl  Linear Multiple Output Sparse Group Lasso 
lsmeans  LeastSquares Means 
ltsa  Linear Time Series Analysis 
lubridate  Make Dealing with Dates a Little Easier 
magic  Create and Investigate Magic Squares 
magrittr  A ForwardPipe Operator for R 
MAIT  Statistical Analysis of Metabolomic Data 
MALDIquant  Quantitative Analysis of Mass Spectrometry Data 
manipulate  Interactive Plots for RStudio 
manipulateWidget  Add Even More Interactivity to Interactive Charts 
mapdata  Extra Map Databases 
mapedit  Interactive Editing of Spatial Data in R 
mapproj  Map Projections 
maps  Draw Geographical Maps 
maptools  Tools for Reading and Handling Spatial Objects 
mapview  Interactive Viewing of Spatial Data in R 
markdown  'Markdown' Rendering for R 
MARSS  Multivariate Autoregressive StateSpace Modeling 
MASS  Support Functions and Datasets for Venables and Ripley's MASS 
MassSpecWavelet  Mass spectrum processing by waveletbased algorithms 
Matrix  Sparse and Dense Matrix Classes and Methods 
matrixcalc  Collection of functions for matrix calculations 
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 
mclust  Gaussian Mixture Modelling for ModelBased Clustering 
mcmc  Markov Chain Monte Carlo 
MCMCpack  Markov Chain Monte Carlo (MCMC) Package 
mcmcplots  Create Plots from MCMC Output 
mda  Mixture and Flexible Discriminant Analysis 
mdatools  Multivariate Data Analysis for Chemometrics 
memoise  Memoisation of Functions 
memuse  Memory Estimation Utilities 
MESS  Miscellaneous Esoteric Statistical Scripts 
metabolomics  Analysis of Metabolomics Data 
MetaboSignal  MetaboSignal: a networkbased approach to overlay and explore metabolic and signaling KEGG pathways 
metap  MetaAnalysis of Significance Values 
methylKit  DNA methylation analysis from highthroughput bisulfite sequencing results 
methylumi  Handle Illumina methylation data 
Metrics  Evaluation Metrics for Machine Learning 
mgcv  Mixed GAM Computation Vehicle with Automatic Smoothness Estimation 
mice  Multivariate Imputation by Chained Equations 
micropan  Microbial PanGenome Analysis 
microseq  Basic Biological Sequence Handling 
mime  Map Filenames to MIME Types 
minfi  Analyze Illumina Infinium DNA methylation arrays 
miniUI  Shiny UI Widgets for Small Screens 
minpack.lm  R Interface to the LevenbergMarquardt Nonlinear LeastSquares Algorithm Found in MINPACK 
minqa  Derivativefree optimization algorithms by quadratic approximation 
mirt  Multidimensional Item Response Theory 
misc3d  Miscellaneous 3D Plots 
miscTools  Miscellaneous Tools and Utilities 
missForest  Nonparametric Missing Value Imputation using Random Forest 
mitml  Tools for Multiple Imputation in Multilevel Modeling 
mitools  Tools for multiple imputation of missing data 
mixOmics  Omics Data Integration Project 
mixtools  Tools for Analyzing Finite Mixture Models 
mlbench  Machine Learning Benchmark Problems 
mnormt  The Multivariate Normal and t Distributions 
ModelMetrics  Rapid Calculation of Model Metrics 
modelr  Modelling Functions that Work with the Pipe 
modeltools  Tools and Classes for Statistical Models 
mpm  Multivariate Projection Methods 
mpoly  Symbolic Computation and More with Multivariate Polynomials 
msm  MultiState Markov and Hidden Markov Models in Continuous Time 
MSnbase  Base Functions and Classes for Mass Spectrometry and Proteomics 
MTS  AllPurpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models 
multcomp  Simultaneous Inference in General Parametric Models 
multispatialCCM  Multispatial Convergent Cross Mapping 
multiwayvcov  MultiWay Standard Error Clustering 
multtest  Resamplingbased multiple hypothesis testing 
munsell  Utilities for Using Munsell Colours 
mvtnorm  Multivariate Normal and t Distributions 
MWASTools  MWASTools: an integrated pipeline to perform metabolomewide association studies 
mygene  Access MyGene.Info_ services 
mzID  An mzIdentML parser for R 
mzR  parser for netCDF 
NADA  Nondetects and Data Analysis for Environmental Data 
natserv  'NatureServe' Interface 
ncbit  retrieve and build NBCI taxonomic data 
ncvreg  Regularization Paths for SCAD and MCP Penalized Regression Models 
neldermead  R Port of the 'Scilab' Neldermead Module 
network  Classes for Relational Data 
neuralnet  Training of Neural Networks 
nleqslv  Solve Systems of Nonlinear Equations 
nlme  Linear and Nonlinear Mixed Effects Models 
nloptr  R interface to NLopt 
NLP  Natural Language Processing Infrastructure 
NMF  Algorithms and Framework for Nonnegative Matrix Factorization (NMF) 
nnet  FeedForward Neural Networks and Multinomial LogLinear Models 
NOISeq  Exploratory analysis and differential expression for RNAseq data 
nor1mix  Normal (1d) Mixture Models (S3 Classes and Methods) 
np  Nonparametric Kernel Smoothing Methods for Mixed Data Types 
numDeriv  Accurate Numerical Derivatives 
oligo  Preprocessing tools for oligonucleotide arrays 
oligoClasses  Classes for highthroughput arrays supported by oligo and crlmm 
openNLP  Apache OpenNLP Tools Interface 
openNLPdata  Apache OpenNLP Jars and Basic English Language Models 
openssl  Toolkit for Encryption 
openxlsx  Read 
optextras  Tools to Support Optimization Possibly with Bounds and Masks 
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 
ordinal  Regression Models for Ordinal Data 
ordinationDuality  Performs orthogonal decomposition 
OrganismDbi  Software to enable the smooth interfacing of different database packages 
org.Hs.eg.db  Genome wide annotation for Human 
orthopolynom  Collection of functions for orthogonal and orthonormal polynomials 
packrat  A Dependency Management System for Projects and their R Package Dependencies 
pamr  Pam: prediction analysis for microarrays 
pan  Multiple Imputation for Multivariate Panel or Clustered Data 
parallelDist  Parallel Distance Matrix Computation using Multiple Threads 
partitions  Additive Partitions of Integers 
pbapply  Adding Progress Bar to '*apply' Functions 
pbdZMQ  Programming with Big Data  Interface to 'ZeroMQ' 
pbivnorm  Vectorized Bivariate Normal CDF 
pbkrtest  Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison 
pbmcapply  Tracking the Progress of Mc*pply with Progress Bar 
pcalg  Methods for Graphical Models and Causal Inference 
pcaMethods  A collection of PCA methods 
pcaPP  Robust PCA by Projection Pursuit 
pegas  Population and Evolutionary Genetics Analysis System 
penalized  L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation in GLMs and in the Cox Model 
PerformanceAnalytics  Econometric Tools for Performance and Risk Analysis 
permute  Functions for Generating Restricted Permutations of Data 
phangorn  Phylogenetic Reconstruction and Analysis 
pheatmap  Pretty Heatmaps 
phylobase  Base Package for Phylogenetic Structures and Comparative Data 
phylolm  Phylogenetic Linear Regression 
phylomap  Phylogenetic Stochastic Mapping 
phyloseq  Handling and analysis of highthroughput microbiome census data 
phytools  Phylogenetic Tools for Comparative Biology (and Other Things) 
picasso  Pathwise Calibrated Sparse Shooting Algorithm 
pillar  Coloured Formatting for Columns 
pinfsc50  Sequence ('FASTA') 
pixmap  Bitmap Images (``Pixel Maps) 
pkgconfig  Private Configuration for 'R' Packages 
pkgmaker  Development Utilities for R Packages 
PKI  Public Key Infrastucture for R Based on the X.509 Standard 
plogr  The 'plog' C++ Logging Library 
plot3D  Plotting MultiDimensional Data 
plotly  Create Interactive Web Graphics via 'plotly.js' 
plotmo  Plot a Model's Residuals 
plotrix  Various Plotting Functions 
pls  Partial Least Squares and Principal Component Regression 
plsgenomics  PLS Analyses for Genomics 
plsRglm  Partial Least Squares Regression for Generalized Linear Models 
plyr  Tools for Splitting 
png  Read and write PNG images 
polynom  A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations 
PopGenome  An Efficient Swiss Army Knife for Population Genomic Analyses 
pophelper  Tabulate 
poRe  An R package to enable organisation and visualisation of nanopore sequencing data 
poweRlaw  Analysis of Heavy Tailed Distributions 
ppcor  Partial and SemiPartial (Part) Correlation 
prabclus  Functions for Clustering of PresenceAbsence 
pracma  Practical Numerical Math Functions 
praise  Praise Users 
preprocessCore  A collection of preprocessing functions 
PresenceAbsence  PresenceAbsence Model Evaluation. 
prettyunits  Pretty 
pROC  Display and Analyze ROC Curves 
processx  Execute and Control System Processes 
prodlim  ProductLimit Estimation for Censored Event History Analysis 
progress  Terminal Progress Bars 
proj4  A simple interface to the PROJ.4 cartographic projections library 
promises  Abstractions for PromiseBased Asynchronous Programming 
propr  Calculating Proportionality Between Vectors of Compositional Data 
ProtGenerics  S4 generic functions for Bioconductor proteomics infrastructure 
proto  Prototype ObjectBased Programming 
proxy  Distance and Similarity Measures 
pryr  Tools for Computing on the Language 
pscl  Political Science Computational Laboratory 
psych  Procedures for Psychological 
purrr  Functional Programming Tools 
purrrlyr  Tools at the Intersection of 'purrr' and 'dplyr' 
qdap  Bridging the Gap Between Qualitative Data and Quantitative Analysis 
qdapDictionaries  Dictionaries and Word Lists for the 'qdap' Package 
qdapRegex  Regular Expression Removal 
qdapTools  Tools for the 'qdap' Package 
qpcR  Modelling and Analysis of RealTime PCR Data 
qqman  QQ and Manhattan Plots for GWAS Data 
qtl  Tools for Analyzing QTL Experiments 
quadprog  Functions to solve Quadratic Programming Problems. 
quantmod  Quantitative Financial Modelling Framework 
quantreg  Quantile Regression 
questionr  Functions to Make Surveys Processing Easier 
qvalue  Qvalue estimation for false discovery rate control 
R2admb  'ADMB' to R Interface Functions 
R2GUESS  Wrapper Functions for GUESS 
R2HTML  HTML Exportation for R Objects 
R2jags  Using R to Run 'JAGS' 
R2WinBUGS  Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'SPLUS' 
R6  Classes with Reference Semantics 
radiator  RADseq Data Exploration 
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 
randtoolbox  Toolbox for Pseudo and Quasi Random Number Generation and RNG Tests 
ranger  A Fast Implementation of Random Forests 
RANN  Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric 
rARPACK  Solvers for Large Scale Eigenvalue and SVD Problems 
raster  Geographic Data Analysis and Modeling 
rasterVis  Visualization Methods for Raster Data 
R.basic  [R] Class Library  Standalone basic functions [DEPRECATED] 
RBGL  An interface to the BOOST graph library 
Rcgmin  Conjugate Gradient Minimization of Nonlinear 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 
RcppGSL  'Rcpp' Integration for 'GNU GSL' Vectors and Matrices 
RcppParallel  Parallel Programming Tools for 'Rcpp' 
RcppProgress  An Interruptible Progress Bar with OpenMP Support for C++ in R Packages 
RcppRoll  Efficient Rolling / Windowed Operations 
RcppZiggurat  'Rcpp' Integration of Different "Ziggurat" Normal RNG Implementations 
RCurl  General Network (HTTP/FTP/...) Client Interface for R 
rda  Shrunken Centroids Regularized Discriminant Analysis 
R.devices  Unified Handling of Graphics Devices 
readr  Read Rectangular Text Data 
readxl  Read Excel Files 
recipes  Preprocessing Tools to Create Design Matrices 
registry  Infrastructure for R Package Registries 
regress  Gaussian Linear Models with Linear Covariance Structure 
rematch  Match Regular Expressions with a Nicer 'API' 
rentrez  'Entrez' in R 
reports  Assist the Workflow of Writing Academic Articles and Other Reports 
repr  Serializable Representations 
reprex  Prepare Reproducible Example Code via the Clipboard 
reshape  Flexibly Reshape Data 
reshape2  Flexibly Reshape Data: A Reboot of the Reshape Package 
ResourceSelection  Resource Selection (Probability) Functions for UseAvailability Data 
reticulate  Interface to 'Python' 
rex  Friendly Regular Expressions 
rexpokit  R Wrappers for EXPOKIT; Other Matrix Functions 
rgdal  Bindings for the 'Geospatial' Data Abstraction Library 
rgeos  Interface to Geometry Engine  Open Source ('GEOS') 
rgl  3D Visualization Using OpenGL 
Rgraphviz  Provides plotting capabilities for R graph objects 
rhdf5  HDF5 interface to R 
rhierbaps  rhierbaps 
RhpcBLASctl  Control the Number of Threads on 'BLAS' 
Rhtslib  HTSlib highthroughput sequencing library as an R package 
RInside  C++ Classes to Embed R in C++ Applications 
rio  A SwissArmy Knife for Data I/O 
ritis  Integrated Taxonomic Information System Client 
rjags  Bayesian Graphical Models using MCMC 
rJava  LowLevel R to Java Interface 
rjson  JSON for R 
RJSONIO  Serialize R objects to JSON 
rlang  Functions for Base Types and Core R and 'Tidyverse' Features 
rlas  Read and Write 'las' and 'laz' Binary File Formats Used for Remote Sensing Data 
rlecuyer  R Interface to RNG with Multiple Streams 
rmarkdown  Dynamic Documents for R 
R.methodsS3  S3 Methods Simplified 
Rmisc  Rmisc: Ryan Miscellaneous 
RMTstat  Distributions 
RMySQL  Database Interface and 'MySQL' Driver for R 
RnBeads  RnBeads 
rncl  An Interface to the Nexus Class Library 
RNeXML  Semantically Rich I/O for the 'NeXML' Format 
rngtools  Utility Functions for Working with Random Number Generators 
rngWELL  Toolbox for WELL Random Number Generators 
robust  Port of the S+ "Robust Library" 
robustbase  Basic Robust Statistics 
ROC  utilities for ROC 
ROCR  Visualizing the Performance of Scoring Classifiers 
R.oo  R ObjectOriented Programming with or without References 
rotl  Interface to the 'Open Tree of Life' API 
roxygen2  InLine Documentation for R 
rpart  Recursive Partitioning and Regression Trees 
RPMM  Recursively Partitioned Mixture Model 
RPostgreSQL  R Interface to the 'PostgreSQL' Database System 
rprojroot  Finding Files in Project Subdirectories 
rrBLUP  Ridge Regression and Other Kernels for Genomic Selection 
rrcov  Scalable Robust Estimators with High Breakdown Point 
rredlist  'IUCN' Red List Client 
rrpack  ReducedRank Regression 
Rsamtools  Binary alignment (BAM) 
rsconnect  Deployment Interface for R Markdown Documents and Shiny Applications 
RSkittleBrewer  Fun with R Colors 
rslurm  Submit R Calculations to a Slurm Cluster 
rsm  ResponseSurface Analysis 
Rsolnp  General NonLinear Optimization 
RSpectra  Solvers for LargeScale Eigenvalue and SVD Problems 
RSQLite  'SQLite' Interface for R 
rstan  R Interface to Stan 
rstanarm  Bayesian Applied Regression Modeling via Stan 
rstantools  Tools for Developing R Packages Interfacing with 'Stan' 
rstudioapi  Safely Access the RStudio API 
Rsubread  Subread sequence alignment for R 
rtracklayer  R interface to genome annotation files and the UCSC genome browser 
Rtsne  TDistributed Stochastic Neighbor Embedding using a BarnesHut Implementation 
RUnit  R Unit Test Framework 
R.utils  Various Programming Utilities 
ruv  Detect and Remove Unwanted Variation using Negative Controls 
rvcheck  R/Package Version Check 
rversions  Query 'R' Versions 
rvest  Easily Harvest (Scrape) Web Pages 
Rvmmin  Variable Metric Nonlinear Function Minimization 
rworldmap  Mapping Global Data 
S4Vectors  S4 implementation of vectorlike and listlike objects 
SALES  Elastic Net and (Adaptive) Lasso Penalized Sparse Asymmetric Least Squares (SALES) and Coupled Sparse Asymmetric Least Squares (COSALES) using Coordinate Descent and Proximal Gradient Algorithms 
samr  SAM: Significance Analysis of Microarrays 
sandwich  Robust Covariance Matrix Estimators 
satellite  Handling and Manipulating Remote Sensing Data 
scales  Scale Functions for Visualization 
scatterplot3d  3D Scatter Plot 
scoringRules  Scoring Rules for Parametric and Simulated Distribution Forecasts 
SDMTools  Species Distribution Modelling Tools: Tools for processing data associated with species distribution modelling exercises 
seegSDM  Streamlined Functions for Species Distribution Modelling in the SEEG Research Group 
segmented  Regression Models with BreakPoints / ChangePoints Estimation 
selectr  Translate CSS Selectors to XPath Expressions 
sensitivity  Global Sensitivity Analysis of Model Outputs 
seqinr  Biological Sequences Retrieval and Analysis 
setRNG  Set (Normal) Random Number Generator and Seed 
settings  Software Option Settings Manager for R 
Seurat  Tools for Single Cell Genomics 
sf  Simple Features for R 
sfsmisc  Utilities from 'Seminar fuer Statistik' ETH Zurich 
sglOptim  Generic Sparse Group Lasso Solver 
shape  Functions for Plotting Graphical Shapes 
shiny  Web Application Framework for R 
shinyjs  Easily Improve the User Experience of Your Shiny Apps in Seconds 
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 
SimCorMultRes  Simulates Correlated Multinomial Responses 
SKAT  SNPSet (Sequence) Kernel Association Test 
slam  Sparse Lightweight Arrays and Matrices 
sleuth  Tools for investigating RNASeq 
sn  The SkewNormal and Related Distributions Such as the Skewt 
sna  Tools for Social Network Analysis 
snow  Simple Network of Workstations 
snowfall  Easier cluster computing (based on snow). 
snpReady  Preparing Genotypic Datasets in Order to Run Genomic Analysis 
SNPRelate  Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data 
snpStats  SnpMatrix and XSnpMatrix classes and methods 
solrium  General Purpose R Interface to 'Solr' 
sommer  Solving Mixed Model Equations in R 
sourcetools  Tools for Reading 
sp  Classes and Methods for Spatial Data 
spacetime  Classes and Methods for SpatioTemporal Data 
spam  SPArse Matrix 
sparsebn  Learning Sparse Bayesian Networks from HighDimensional Data 
sparsebnUtils  Utilities for Learning Sparse Bayesian Networks 
SparseM  Sparse Linear Algebra 
sparsevar  A Package for Sparse VAR/VECM Estimation 
spatial  Functions for Kriging and Point Pattern Analysis 
SpatioTemporal  SpatioTemporal Model Estimation 
spData  Datasets for Spatial Analysis 
spDataLarge  Large datasets for spatial analysis 
spdep  Spatial Dependence: Weighting Schemes 
speedglm  Fitting Linear and Generalized Linear Models to Large Data Sets 
SpiecEasi  Sparse Inverse Covariance for Ecological Statistical Inference 
splancs  Spatial and SpaceTime Point Pattern Analysis 
splitstackshape  Stack and Reshape Datasets After Splitting Concatenated Values 
spls  Sparse Partial Least Squares (SPLS) Regression and Classification 
sqldf  Manipulate R Data Frames Using SQL 
SQUAREM  Squared Extrapolation Methods for Accelerating EMLike Monotone Algorithms 
stabledist  Stable Distribution Functions 
StanHeaders  C++ Header Files for Stan 
statip  Statistical Functions for Probability Distributions 
statmod  Statistical Modeling 
statnet.common  Common R Scripts and Utilities Used by the Statnet Project Software 
stringdist  Approximate String Matching and String Distance Functions 
stringi  Character String Processing Facilities 
stringr  Simple 
strucchange  Testing 
subplex  Unconstrained Optimization using the Subplex Algorithm 
SummarizedExperiment  SummarizedExperiment container 
survey  Analysis of Complex Survey Samples 
survival  Survival Analysis 
sva  Surrogate Variable Analysis 
svDialogs  'SciViews'  Standard Dialog Boxes for Windows 
SVGAnnotation  Tools for postprocessing SVG plots created in R 
svglite  An 'SVG' Graphics Device 
svGUI  SciViews  Manage GUIs in R 
svUnit  SciViews GUI API  Unit testing 
symDMatrix  Partitioned Symmetric Matrices 
synbreed  Framework for the Analysis of Genomic Prediction Data using R 
targetSeqView  View alignments over candidate structural variant loci 
tawny  Clean Covariance Matrices Using Random Matrix Theory and Shrinkage Estimators for Portfolio Optimization 
tawny.types  Common Types for Tawny 
taxize  Taxonomic Information from Around the Web 
tclust  Robust Trimmed Clustering 
TeachingDemos  Demonstrations for Teaching and Learning 
tensorA  Advanced tensors arithmetic with named indices 
tensorflow  R Interface to 'TensorFlow' 
testthat  Unit Testing for R 
tfruns  Training Run Tools for 'TensorFlow' 
TH.data  TH's Data Archive 
threejs  Interactive 3D Scatter Plots 
tibble  Simple Data Frames 
tidyr  Easily Tidy Data with 'spread()' and 'gather()' Functions 
tidyselect  Select from a Set of Strings 
tidyverse  Easily Install and Load the 'Tidyverse' 
tiff  Read and write TIFF images 
timeDate  Rmetrics  Chronological and Calendar Objects 
timeSeries  Rmetrics  Financial Time Series Objects 
tinytex  Helper Functions to Install and Maintain 'TeX Live' 
tm  Text Mining Package 
treeio  Base Classes and Functions for Phylogenetic Tree Input and Output 
triebeard  'Radix' Trees in 'Rcpp' 
trimcluster  Cluster analysis with trimming 
truncnorm  Truncated Normal Distribution 
tseries  Time Series Analysis and Computational Finance 
tseriesChaos  Analysis of nonlinear time series 
tsne  TDistributed Stochastic Neighbor Embedding for R (tSNE) 
TTR  Technical Trading Rules 
twang  Toolkit for Weighting and Analysis of Nonequivalent Groups 
TxDb.Hsapiens.UCSC.hg19.knownGene  Annotation package for TxDb object(s) 
ucminf  GeneralPurpose Unconstrained NonLinear Optimization 
udunits2  Udunits2 Bindings for R 
units  Measurement Units for R Vectors 
UpSetR  A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets 
urca  Unit Root and Cointegration Tests for Time Series Data 
urltools  Vectorised Tools for URL Handling and Parsing 
uroot  Unit Root Tests for Seasonal Time Series 
utf8  Unicode Text Processing 
uuid  Tools for generating and handling of UUIDs 
V8  Embedded JavaScript Engine for R 
VariantAnnotation  Annotation of Genetic Variants 
vars  VAR Modelling 
varSelRF  Variable Selection using Random Forests 
vcd  Visualizing Categorical Data 
vcfR  Manipulate and Visualize VCF Data 
vegan  Community Ecology Package 
VEGAWES  A package to perform vartiationalbased copy number segmentation on WES data 
VennDiagram  Generate HighResolution Venn and Euler Plots 
venneuler  Venn and Euler Diagrams 
VGAM  Vector Generalized Linear and Additive Models 
viridis  Default Color Maps from 'matplotlib' 
viridisLite  Default Color Maps from 'matplotlib' (Lite Version) 
vsn  Variance stabilization and calibration for microarray data 
wavelets  A package of functions for computing wavelet filters 
waveslim  Basic wavelet routines for one 
wavethresh  Wavelets Statistics and Transforms 
wbs  Wild Binary Segmentation for Multiple ChangePoint Detection 
webshot  Take Screenshots of Web Pages 
WGCNA  Weighted Correlation Network Analysis 
whisker  {{mustache}} for R 
WikidataR  API Client Library for 'Wikidata' 
WikipediR  A MediaWiki API Wrapper 
wikitaxa  Taxonomic Information from 'Wikipedia' 
withr  Run Code 'With' Temporarily Modified Global State 
wordcloud  Word Clouds 
worrms  World Register of Marine Species (WoRMS) Client 
xcms  LC/MS and GC/MS Data Analysis 
xgboost  Extreme Gradient Boosting 
xlsx  Read 
xlsxjars  Package required POI jars for the xlsx package 
XML  Tools for Parsing and Generating XML Within R and SPlus 
xml2  Parse XML 
xtable  Export Tables to LaTeX or HTML 
xts  eXtensible Time Series 
XVector  Representation and manipulation of external sequences 
yaml  Methods to Convert R Data to YAML and Back 
zCompositions  Treatment of Zeros and Nondetects in Compositional Data Sets 
zeallot  Multiple 
zip  CrossPlatform 'zip' Compression 
zlibbioc  An R packaged zlib1.2.5 
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 Automatic Smoothness Estimation 
nlme  Linear and Nonlinear Mixed Effects Models 
nnet  FeedForward Neural Networks and Multinomial LogLinear 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 
FAQ
 Q: When I submit the job with N=1 and M=1 it runs and R allocates the 10 slaves that I want. Is this the OK?
 A: In short, no. This is bad since you are lying to the scheduler about the resources you intend to run. We have scripts that will kill your job if they catch it and we tend to suspend accounts of users who make a practice of it. :)
 Q: The actual job I want to run is much larger. Anywhere from 31 to 93 processors are desired. Is it ok to request this many processors.
 A: That depends on the level of investment from your PI. If you ask for processors than your groups core allocation, which depends on the investment level, you will be essentially borrowing cores from other groups and may wait an extended period of time in the queue before your job runs. Groups are allowed to run on up to 10x their core allocation provided the resources are available. If you ask for more than 10x your groups core allocation, the job will be blocked indefinitely.
 Q: Do I need the number of nodes requested to be correct or can I just have R go grab slaves after the job is submitted with N=1 and M=1?
 A: Your resource request must be consistent with what you actually intend to use as noted above.
 Q: Is it better to request a large number of nodes for a shorter period of time or less nodes for longer period of time (concretely, say 8 nodes for 40 hours versus 16 nodes for 20 hours) in terms of getting through the queue?
 A: Do not confuse "nodes" with "cores/processors". Each "node" is a physical machine with between 4 and 48 cores. Your MPI threads will run on "cores" which may all be in the same "node" or spread among multiple nodes. You should ask for the number of cores you need and spread them among as few nodes as possible unless you have a good reason to do otherwise. Thus you should generally ask for things like
#PBS l nodes=1:ppn=8 (we have lots of 8p nodes) #PBS l nodes=1:ppn=12 (we have a number of 12p also)
Multiples of the above work as well so you might ask for nodes=3:ppn=8 if you want to run 24 threads on 24 different cores. It looks like in the R model there is a master/slave paradigm so you really need one master thread to manage the "slave" threads. It is likely that the master thread accumulates little CPU time so you could neglect it. In other words tell the scheduler that you want nodes=3:ppn=8 and tell R to spawn 24 children. This is a white lie which will do little harm. However, if it turns out that the master accumulates significant CPU time and your job gets killed by our rogue process killer, you can ask for the resources as follows
#PBS l nodes=1:ppn=1infiniband+3:ppn=8:infiniband
This will allocate 1 thread on a separate node (the master thread) and then the slave threads will be allocated on 3 additional nodes with at least 8 cores each.
 A: Do not confuse "nodes" with "cores/processors". Each "node" is a physical machine with between 4 and 48 cores. Your MPI threads will run on "cores" which may all be in the same "node" or spread among multiple nodes. You should ask for the number of cores you need and spread them among as few nodes as possible unless you have a good reason to do otherwise. Thus you should generally ask for things like
Rmpi Example
Example of using the parallel module to run MPI jobs under R 2.14.1+
{{#fileAnchor: rmpi_test.R}} Download raw source of the [{{#fileLink: rmpi_test.R}} rmpi_test.R] file.
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
# Spawn as many slaves as possible
mpi.spawn.Rslaves()
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last < function(){
if (is.loaded("mpi_initialize")){
if (mpi.comm.size(1) > 0){
print("Please use mpi.close.Rslaves() to close slaves.")
mpi.close.Rslaves()
}
print("Please use mpi.quit() to quit R")
.Call("mpi_finalize")
}
}
# Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves()
mpi.quit()