R

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.

Environment Modules

Run module spider R to find out what environment modules are available for this application.

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. Alternatively an instance of RStudio Server can be started in a job. Then you can connect to it through an SSH tunnel from a web browser on your local computer.

Notes and Warnings

• The parallel::detectCores() function will return the total number of cores on a compute node and not the number of cores assigned to your job by the scheduler. Instead, use something like

numCores = as.integer(Sys.getenv("SLURM_CPUS_ON_NODE"))

to find out the number of CPU cores 'X' requested by

#SBATCH --cpus-per-task=X

in your job script.

• Default RData format

In R-3.6.0 the default serialization format used to save RData files has been changed to version 3 (RDX3), so R versions prior to 3.5.0 will not be able to open it. Keep this in mind if you copy RData files from HiPerGator to an external system with old R installed.

• 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

• Q: How do I install R packages?
  • A: Users can install R packages in their local directory. The default directory is /home/my.username/R/x86_64-pc-linux-gnu-library/X.X/ (X.X = version number)

From a tarball:

# from a standard repository
$ module load R/X.X
$ R
> install.packages("PACKAGE")
if coming from github
> devtools::install_github("author/software")

# from a non-standard repository (tarball available)
$ module load R/X.X

$ R CMD INSTALL /path/to/package_version.tar.gz

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
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	No-U-Turn 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 probe-level 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	Light-Weight 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 R-3.0.0
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/Micro-Econometrics
bayesplot	Plotting for Bayesian Models
bazar	Miscellaneous Basic Functions
BB	Solving and Optimizing Large-Scale Nonlinear Systems
bbmle	Tools for General Maximum Likelihood Estimation
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)
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 larger-than-RAM data.frame-like objects in R.
biglm	bounded memory linear and generalized linear models
bigmemory	Manage Massive Matrices with Shared Memory and Memory-Mapped 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 1-Bit 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 high-quality 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 Non-Repeated) 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	Composite-Likelihood 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 Matrix-Like Types
crosstalk	Inter-Widget Interactivity for HTML Widgets
crul	HTTP Client
cubature	Adaptive Multivariate Integration over Hypercubes
curl	A Modern and Flexible Web Client for R
CVST	Fast Cross-Validation via Sequential Testing
cvTools	Cross-validation tools for regression models
dagitty	Graphical Analysis of Structural Causal Models
DASTool	DAS Tool - Dereplication Aggregation and Scoring Tool for genome-resolved metagenomics
DatABEL	File-Based 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	Depth-Based Classification and Calculation of Data Depth
debugme	Debug R Packages
DelayedArray	Delayed operations on array-like 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	Derivative-Free 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	Coordinate-Descent 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 RNA-Seq 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 RNA-seq data
edgeR	Empirical Analysis of Digital Gene Expression Data in R
eDNAoccupancy	Multi-scale Occupancy Modeling of Environmental DNA Data
egg	Extensions for 'ggplot2': Custom Geom
ellipse	Functions for Drawing Ellipses and Ellipse-Like Confidence Regions
emdbook	Support Functions and Data for "Ecological Models and Data"
emulator	Bayesian Emulation of Computer Programs
energy	E-Statistics: Multivariate Inference via the Energy of Data
EnsDb.Hsapiens.v75	Ensembl based annotation package
ensembldb	Utilities to create and use Ensembl-based 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	Memory-Efficient Storage of Large Data on Disk and Fast Access Functions
fftwtools	Wrapper for 'FFTW3' Includes: One-Dimensional 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 Non-Censored 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	genome-wide 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 high-throughput 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	C-Like 'getopt' Behavior
GetoptLong	Parsing Command-Line 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 Non-Overlapping Text Labels with 'ggplot2'
ggridges	Ridgeline Plots in 'ggplot2'
ggsci	Scientific Journal and Sci-Fi 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 L1-Penalized Estimation
glmnet	Lasso and Elastic-Net 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	GO-terms 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 Spatio-Temporal 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	Hurst-Kolmogorov 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	High-Dimensional Undirected Graph Estimation
hunspell	High-Performance Stemmer
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
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	Kernel-Based 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 multi-types and multi-groups expression data in KEGG pathway
KEGGREST	Client-side REST access to KEGG
keras	R Interface to 'Keras'
kerasR	R Interface to the Keras Deep Learning Library
kernlab	Kernel-Based 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 General-Purpose 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 (Non-Standard) 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	Column-Linked and Row-Linked Matrices
lintr	A 'Linter' for R Code
listenv	Environments Behaving (Almost) as Lists
lme4	Linear Mixed-Effects Models using 'Eigen' and S4
lmmen	Linear Mixed Model Elastic Net
lmmlasso	Linear mixed-effects models with Lasso
lmtest	Testing Linear Regression Models
locfit	Local Regression
loo	Efficient Leave-One-Out Cross-Validation 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	Least-Squares Means
ltsa	Linear Time Series Analysis
lubridate	Make Dealing with Dates a Little Easier
magic	Create and Investigate Magic Squares
magrittr	A Forward-Pipe 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 State-Space Modeling
MASS	Support Functions and Datasets for Venables and Ripley's MASS
MassSpecWavelet	Mass spectrum processing by wavelet-based 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 Model-Based 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 network-based approach to overlay and explore metabolic and signaling KEGG pathways
metap	Meta-Analysis of Significance Values
methylKit	DNA methylation analysis from high-throughput 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 Pan-Genome 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 Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK
minqa	Derivative-free 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	Multi-State Markov and Hidden Markov Models in Continuous Time
MSnbase	Base Functions and Classes for Mass Spectrometry and Proteomics
MTS	All-Purpose 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	Multi-Way Standard Error Clustering
multtest	Resampling-based multiple hypothesis testing
munsell	Utilities for Using Munsell Colours
mvtnorm	Multivariate Normal and t Distributions
MWASTools	MWASTools: an integrated pipeline to perform metabolome-wide 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	Feed-Forward Neural Networks and Multinomial Log-Linear Models
NOISeq	Exploratory analysis and differential expression for RNA-seq data
nor1mix	Normal (1-d) 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 high-throughput 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 high-throughput 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 Multi-Dimensional 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 Semi-Partial (Part) Correlation
prabclus	Functions for Clustering of Presence-Absence
pracma	Practical Numerical Math Functions
praise	Praise Users
preprocessCore	A collection of pre-processing functions
PresenceAbsence	Presence-Absence Model Evaluation.
prettyunits	Pretty
pROC	Display and Analyze ROC Curves
processx	Execute and Control System Processes
prodlim	Product-Limit Estimation for Censored Event History Analysis
progress	Terminal Progress Bars
proj4	A simple interface to the PROJ.4 cartographic projections library
promises	Abstractions for Promise-Based Asynchronous Programming
propr	Calculating Proportionality Between Vectors of Compositional Data
ProtGenerics	S4 generic functions for Bioconductor proteomics infrastructure
proto	Prototype Object-Based 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 Real-Time PCR Data
qqman	Q-Q 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	Q-value 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' / 'S-PLUS'
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 - Stand-alone 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 Use-Availability 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 high-throughput sequencing library as an R package
RInside	C++ Classes to Embed R in C++ Applications
rio	A Swiss-Army Knife for Data I/O
ritis	Integrated Taxonomic Information System Client
rjags	Bayesian Graphical Models using MCMC
rJava	Low-Level 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 Object-Oriented Programming with or without References
rotl	Interface to the 'Open Tree of Life' API
roxygen2	In-Line 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	Reduced-Rank 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	Response-Surface Analysis
Rsolnp	General Non-Linear Optimization
RSpectra	Solvers for Large-Scale 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	T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut 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 vector-like and list-like 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 Break-Points / Change-Points 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	SNP-Set (Sequence) Kernel Association Test
slam	Sparse Lightweight Arrays and Matrices
sleuth	Tools for investigating RNA-Seq
sn	The Skew-Normal and Related Distributions Such as the Skew-t
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 Spatio-Temporal Data
spam	SPArse Matrix
sparsebn	Learning Sparse Bayesian Networks from High-Dimensional 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	Spatio-Temporal 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 Space-Time 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 EM-Like 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 post-processing 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	T-Distributed Stochastic Neighbor Embedding for R (t-SNE)
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	General-Purpose Unconstrained Non-Linear Optimization
udunits2	Udunits-2 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 vartiational-based copy number segmentation on WES data
VennDiagram	Generate High-Resolution 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 Change-Point 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 S-Plus
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	Cross-Platform 'zip' Compression
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 Automatic 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