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R and Bioconductor Packages installed on RC Systemsยง

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This is a list of the R add-on packages available with R 3.4.0 and Bioconductor 3.5 on Legion, Grace, Thomas and Aristotle.

Package Description
abc Tools for Approximate Bayesian Computation (ABC)
abc.data Data Only: Tools for Approximate Bayesian Computation (ABC)
abind Combine Multidimensional Arrays
acepack ACE and AVAS for Selecting Multiple Regression Transformations
adapt adapt -- multidimensional numerical integration
ade4 Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
adegenet Exploratory Analysis of Genetic and Genomic Data
ADGofTest Anderson-Darling GoF test
affxparser Affymetrix File Parsing SDK
affy Methods for Affymetrix Oligonucleotide Arrays
affydata Affymetrix Data for Demonstration Purpose
affyio Tools for parsing Affymetrix data files
affylmGUI GUI for limma package with Affymetrix microarrays
affyPLM Methods for fitting probe-level models
affyQCReport QC Report Generation for affyBatch objects
akima Interpolation of Irregularly and Regularly Spaced Data
annaffy Annotation tools for Affymetrix biological metadata
annmap Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annotate Annotation for microarrays
AnnotationDbi Annotation Database Interface
AnnotationForge Code for Building Annotation Database Packages
AnnotationHub Client to access AnnotationHub resources
ape Analyses of Phylogenetics and Evolution
aroma.affymetrix Analysis of Large Affymetrix Microarray Data Sets
aroma.apd A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
aroma.core Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
assertthat Easy pre and post assertions.
backports Reimplementations of Functions Introduced Since R-3.0.0
base The R Base Package
base64 Base64 Encoder and Decoder
base64enc Tools for base64 encoding
BaSTA Age-Specific Survival Analysis from Incomplete Capture-Recapture/Recovery Data
BatchJobs Batch Computing with R
bayesplot Plotting for Bayesian Models
BBmisc Miscellaneous Helper Functions for B. Bischl
beadarray Quality assessment and low-level analysis for Illumina BeadArray data
beadarrayExampleData Example data for the beadarray package
BeadDataPackR Compression of Illumina BeadArray data
beanplot Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot)
BH Boost C++ Header Files
BiasedUrn Biased Urn Model Distributions
Biobase Biobase: Base functions for Bioconductor
BiocGenerics S4 generic functions for Bioconductor
BiocInstaller Install/Update Bioconductor, CRAN, and github Packages
BiocParallel Bioconductor facilities for parallel evaluation
biomaRt Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)
Biostrings String objects representing biological sequences, and matching algorithms
biovizBase Basic graphic utilities for visualization of genomic data.
bitops Bitwise Operations
blockmodeling An R package for Generalized and classical blockmodeling of valued networks
boot Bootstrap Functions (Originally by Angelo Canty for S)
brew Templating Framework for Report Generation
BSgenome Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation
BSgenome.Hsapiens.UCSC.hg19 Full genome sequences for Homo sapiens (UCSC version hg19)
bsseq Analyze, manage and store bisulfite sequencing data
bumphunter Bump Hunter
car Companion to Applied Regression
caret Classification and Regression Training
Category Category Analysis
caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
ChAMP Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
ChAMPdata Data Packages for ChAMP package
checkmate Fast and Versatile Argument Checks
class Functions for Classification
cluster "Finding Groups in Data": Cluster Analysis Extended Rousseeuw et al.
cmprsk Subdistribution Analysis of Competing Risks
coda Output Analysis and Diagnostics for MCMC
codetools Code Analysis Tools for R
colorRamps Builds color tables
colorspace Color Space Manipulation
colourpicker A Colour Picker Widget for Shiny Apps, RStudio, R-markdown, and 'htmlwidgets'
combinat combinatorics utilities
compiler The R Compiler Package
copula Multivariate Dependence with Copulas
copynumber Segmentation of single- and multi-track copy number data by penalized least squares regression.
corpcor Efficient Estimation of Covariance and (Partial) Correlation
corrplot Visualization of a Correlation Matrix
crayon Colored Terminal Output
curl A Modern and Flexible Web Client for R
data.table Extension of Data.frame
datasets The R Datasets Package
DBI R Database Interface
deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation
dendextend Extending R's Dendrogram Functionality
DEoptimR Differential Evolution Optimization in Pure R
DESeq Differential gene expression analysis based on the negative binomial distribution
DESeq2 Differential gene expression analysis based on the negative binomial distribution
Design Design Package
DEXSeq Inference of differential exon usage in RNA-Seq
dichromat Color Schemes for Dichromats
digest Create Compact Hash Digests of R Objects
diptest Hartigan's Dip Test Statistic for Unimodality - Corrected
DMRcate Methylation array and sequencing spatial analysis methods
DMRcatedata Data Package for DMRcate package
DNAcopy DNA copy number data analysis
doMC Foreach Parallel Adaptor for 'parallel'
doParallel Foreach Parallel Adaptor for the 'parallel' Package
doRNG Generic Reproducible Parallel Backend for foreach Loops
dplyr A Grammar of Data Manipulation
DSS Dispersion shrinakge for sequencing data.
DT A Wrapper of the JavaScript Library 'DataTables'
dygraphs Interface to 'Dygraphs' Interactive Time Series Charting Library
dynamicTreeCut Methods for Detection of Clusters in Hierarchical Clustering Dendrograms
DynDoc Dynamic document tools
e1071 Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien
easyRNASeq Count summarization and normalization for RNA-Seq data
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
effects Effect Displays for Linear, Generalized Linear, and Other Models
ellipse Functions for drawing ellipses and ellipse-like confidence regions
ensembldb Utilities to create and use an Ensembl based annotation database
Epi A Package for Statistical Analysis in Epidemiology
etm Empirical Transition Matrix
evaluate Parsing and Evaluation Tools that Provide More Details than the Default
expm Matrix Exponential
FactoMineR Multivariate Exploratory Data Analysis and Data Mining
fail File Abstraction Interface Layer (FAIL)
fastcluster Fast Hierarchical Clustering Routines for R and Python
fastICA FastICA Algorithms to perform ICA and Projection Pursuit
fastmatch Fast match() function
FDb.InfiniumMethylation.hg19 Annotation package for Illumina Infinium DNA methylation probes
fdrtool Estimation of (Local) False Discovery Rates and Higher Criticism
FEM Identification of Functional Epigenetic Modules
fields Tools for Spatial Data
flashClust Implementation of optimal hierarchical clustering
flexmix Flexible Mixture Modeling
foreach Provides Foreach Looping Construct for R
foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...
Formula Extended Model Formulas
fpc Flexible Procedures for Clustering
futile.logger A Logging Utility for R
futile.options Futile options management
future A Future API for R
gam Generalized Additive Models
gamlss Generalised Additive Models for Location Scale and Shape
gamlss.data GAMLSS Data
gamlss.dist Distributions to be Used for GAMLSS Modelling
gamlss.mx Fitting Mixture Distributions with GAMLSS
gamlss.nl Fitting non linear parametric GAMLSS models
gcrma Background Adjustment Using Sequence Information
gdata Various R Programming Tools for Data Manipulation
GenABEL genome-wide SNP association analysis
GenABEL.data Package contains data which is used by GenABEL example and test functions
genefilter genefilter: methods for filtering genes from high-throughput experiments
geneLenDataBase Lengths of mRNA transcripts for a number of genomes
GeneNet Modeling and Inferring Gene Networks
geneplotter Graphics related functions for Bioconductor
genetics Population Genetics
GenomeGraphs Plotting genomic information from Ensembl
GenomeInfoDb Utilities for manipulating chromosome and other 'seqname' identifiers
genomeIntervals Operations on genomic intervals
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
GEOquery Get data from NCBI Gene Expression Omnibus (GEO)
GGally Extension to 'ggplot2'
ggplot2 Create Elegant Data Visualisations Using the Grammar of Graphics
ggvis Interactive Grammar of Graphics
glmnet Lasso and Elastic-Net Regularized Generalized Linear Models
globals Identify Global Objects in R Expressions
gmodels Various R Programming Tools for Model Fitting
GO.db A set of annotation maps describing the entire Gene Ontology
goseq Gene Ontology analyser for RNA-seq and other length biased data
GOstats Tools for manipulating GO and microarrays.
gplots Various R Programming Tools for Plotting Data
graph graph: A package to handle graph data structures
graphics The R Graphics Package
grDevices The R Graphics Devices and Support for Colours and Fonts
grid The Grid Graphics Package
gridBase Integration of base and grid graphics
gridExtra Miscellaneous Functions for "Grid" Graphics
GSEABase Gene set enrichment data structures and methods
gsl wrapper for the Gnu Scientific Library
gsmoothr Smoothing tools
gtable Arrange 'Grobs' in Tables
gtools Various R Programming Tools
Gviz Plotting data and annotation information along genomic coordinates
HAC Estimation, Simulation and Visualization of Hierarchical Archimedean Copulae (HAC)
haplo.stats Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous
hexbin Hexagonal Binning Routines
hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2)
HI Simulation from distributions supported by nested hyperplanes
highr Syntax Highlighting for R Source Code
Hmisc Harrell Miscellaneous
HotDeckImputation Hot Deck Imputation Methods for Missing Data
htmlTable Advanced Tables for Markdown/HTML
htmltools Tools for HTML
htmlwidgets HTML Widgets for R
httpuv HTTP and WebSocket Server Library
httr Tools for Working with URLs and HTTP
hugene10stprobeset.db Affymetrix hugene10 annotation data (chip hugene10stprobeset)
hugene10sttranscriptcluster.db Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster)
hwriter HTML Writer - Outputs R objects in HTML format
igraph Network Analysis and Visualization
Illumina450ProbeVariants.db Annotation Package combining variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes
IlluminaHumanMethylation450kanno.ilmn12.hg19 Annotation for Illumina's 450k methylation arrays
IlluminaHumanMethylation450kmanifest Annotation for Illumina's 450k methylation arrays
IlluminaHumanMethylationEPICanno.ilm10b2.hg19 Annotation for Illumina's EPIC methylation arrays
IlluminaHumanMethylationEPICmanifest Manifest for Illumina's EPIC methylation arrays
illuminaHumanv4.db Illumina HumanHT12v4 annotation data (chip illuminaHumanv4)
illuminaio Parsing Illumina Microarray Output Files
impute impute: Imputation for microarray data
INLA Functions which Allow to Perform Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations
inline Functions to Inline C, C++, Fortran Function Calls from R
interactiveDisplayBase Base package for enabling powerful shiny web displays of Bioconductor objects
intervals Tools for Working with Points and Intervals
IRanges Infrastructure for manipulating intervals on sequences
irlba Fast Truncated SVD, PCA and Symmetric Eigendecomposition for Large Dense and Sparse Matrices
isva Independent Surrogate Variable Analysis
iterators Provides Iterator Construct for R
jsonlite A Robust, High Performance JSON Parser and Generator for R
KEGG.db A set of annotation maps for KEGG
kernlab Kernel-Based Machine Learning Lab
KernSmooth Functions for Kernel Smoothing Supporting Wand & Jones (1995)
knitr A General-Purpose Package for Dynamic Report Generation in R
labeling Axis Labeling
lambda.r Modeling Data with Functional Programming
lattice Trellis Graphics for R
latticeExtra Extra Graphical Utilities Based on Lattice
lazyeval Lazy (Non-Standard) Evaluation
leaps regression subset selection
LearnBayes Functions for Learning Bayesian Inference
limma Linear Models for Microarray Data
listenv Environments Behaving (Almost) as Lists
lme4 Linear Mixed-Effects Models using 'Eigen' and S4
locfit Local Regression, Likelihood and Density Estimation.
longitudinal Analysis of Multiple Time Course Data
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
LSD Lots of Superior Depictions
lumi BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
made4 Multivariate analysis of microarray data using ADE4
magrittr A Forward-Pipe Operator for R
maps Draw Geographical Maps
maptree Mapping, pruning, and graphing tree models
markdown 'Markdown' Rendering for R
marray Exploratory analysis for two-color spotted microarray data
MASS Support Functions and Datasets for Venables and Ripley's MASS
Matrix Sparse and Dense Matrix Classes and Methods
MatrixModels Modelling with Sparse And Dense Matrices
matrixStats Functions that Apply to Rows and Columns of Matrices (and to Vectors)
mclust Gaussian Mixture Modelling for Model-Based Clustering, Classification, and Density Estimation
mcmc Markov Chain Monte Carlo
memoise Memoisation of Functions
metafor Meta-Analysis Package for R
methods Formal Methods and Classes
methylumi Handle Illumina methylation data
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation
mime Map Filenames to MIME Types
minfi Analyze Illumina Infinium DNA methylation arrays
miniUI Shiny UI Widgets for Small Screens
minqa Derivative-free optimization algorithms by quadratic approximation
missMethyl Analysing Illumina HumanMethylation BeadChip Data
mitools Tools for multiple imputation of missing data
mlr Machine Learning in R
mnormt The Multivariate Normal and t Distributions
ModelMetrics Rapid Calculation of Model Metrics
modeltools Tools and Classes for Statistical Models
msm Multi-State Markov and Hidden Markov Models in Continuous Time
mstate Data Preparation, Estimation and Prediction in Multi-State Models
multcomp Simultaneous Inference in General Parametric Models
multtest Resampling-based multiple hypothesis testing
munsell Utilities for Using Munsell Colours
mvtnorm Multivariate Normal and t Distributions
NetworkAnalysis Statistical inference on populations of weighted or unweighted networks.
nleqslv Solve Systems of Nonlinear Equations
nlme Linear and Nonlinear Mixed Effects Models
nloptr R interface to NLopt
NMF Algorithms and Framework for Nonnegative Matrix Factorization (NMF)
nnet Feed-Forward Neural Networks and Multinomial Log-Linear Models
nnls The Lawson-Hanson algorithm for non-negative least squares (NNLS)
nor1mix Normal (1-d) Mixture Models (S3 Classes and Methods)
numDeriv Accurate Numerical Derivatives
nutshell Data for "R in a Nutshell"
nutshell.audioscrobbler Audioscrobbler data for "R in a Nutshell"
nutshell.bbdb Baseball Database for "R in a Nutshell"
OPE Outer-product emulator
openssl Toolkit for Encryption, Signatures and Certificates Based on OpenSSL
org.Hs.eg.db Genome wide annotation for Human
packrat A Dependency Management System for Projects and their R Package Dependencies
parallel Support for Parallel computation in R
parallelMap Unified Interface to Parallelization Back-Ends
ParamHelpers Helpers for Parameters in Black-Box Optimization, Tuning and Machine Learning
parcor Regularized estimation of partial correlation matrices
pbkrtest Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison
pcaPP Robust PCA by Projection Pursuit
pegas Population and Evolutionary Genetics Analysis System
permute Functions for Generating Restricted Permutations of Data
phangorn Phylogenetic Analysis in R
pixmap Bitmap Images (``Pixel Maps'')
pkgmaker Package development utilities
PKI Public Key Infrastucture for R Based on the X.509 Standard
plogr The 'plog' C++ Logging Library
plotly Create Interactive Web Graphics via 'plotly.js'
pls Partial Least Squares and Principal Component Regression
plyr Tools for Splitting, Applying and Combining Data
polspline Polynomial Spline Routines
poweRlaw Analysis of Heavy Tailed Distributions
ppls Penalized Partial Least Squares
prabclus Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data
pracma Practical Numerical Math Functions
praise Praise Users
preprocessCore A collection of pre-processing functions
prettyunits Pretty, Human Readable Formatting of Quantities
progress Terminal Progress Bars
proto Prototype Object-Based Programming
PSCBS Analysis of Parent-Specific DNA Copy Numbers
pspline Penalized Smoothing Splines
psych Procedures for Psychological, Psychometric, and Personality Research
purrr Functional Programming Tools
quadprog Functions to solve Quadratic Programming Problems.
quantreg Quantile Regression
qvalue Q-value estimation for false discovery rate control
R.cache Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations
R.devices Unified Handling of Graphics Devices
R.filesets Easy Handling of and Access to Files Organized in Structured Directories
R.huge Methods for Accessing Huge Amounts of Data [deprecated]
R.methodsS3 S3 Methods Simplified
R.oo R Object-Oriented Programming with or without References
R.rsp Dynamic Generation of Scientific Reports
R.utils Various Programming Utilities
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
randomForest Breiman and Cutler's Random Forests for Classification and Regression
RBGL An interface to the BOOST graph library
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
RCurl General Network (HTTP/FTP/...) Client Interface for R
RefFreeEWAS EWAS using Reference-Free DNA Methylation Mixture Deconvolution
registry Infrastructure for R Package Registries
relaimpo Relative importance of regressors in linear models
Repitools Epigenomic tools
reshape Flexibly Reshape Data
reshape2 Flexibly Reshape Data: A Reboot of the Reshape Package
rgdal Bindings for the Geospatial Data Abstraction Library
rgeos Interface to Geometry Engine - Open Source (GEOS)
rgl 3D Visualization Using OpenGL
Rglpk R/GNU Linear Programming Kit Interface
ridge Ridge Regression with automatic selection of the penalty parameter
Ringo R Investigation of ChIP-chip Oligoarrays
rjags Bayesian Graphical Models using MCMC
RJSONIO Serialize R objects to JSON, JavaScript Object Notation
rlecuyer R Interface to RNG with Multiple Streams
Rmpi Interface (Wrapper) to MPI (Message-Passing Interface)
rms Regression Modeling Strategies
RMySQL Database Interface and 'MySQL' Driver for R
RNetCDF Interface to NetCDF Datasets
rngtools Utility functions for working with Random Number Generators
robustbase Basic Robust Statistics
ROC utilities for ROC, with uarray focus
rpart Recursive Partitioning and Regression Trees
RPMM Recursively Partitioned Mixture Model
Rsamtools Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
rsconnect Deployment Interface for R Markdown Documents and Shiny Applications
Rsolnp General Non-Linear Optimization
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 browsers and their annotation tracks
ruv Detect and Remove Unwanted Variation using Negative Controls
S4Vectors S4 implementation of vectors and lists
saemix Stochastic Approximation Expectation Maximization (SAEM) algorithm
sampling Survey Sampling
sandwich Robust Covariance Matrix Estimators
scales Scale Functions for Visualization
scatterplot3d 3D Scatter Plot
schoolmath Functions and datasets for math used in school
segmented Regression Models with Breakpoints/Changepoints Estimation
sendmailR send email using R
seqinr Biological Sequences Retrieval and Analysis
seqLogo Sequence logos for DNA sequence alignments
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
simpleaffy Very simple high level analysis of Affymetrix data
slam Sparse Lightweight Arrays and Matrices
sn The Skew-Normal and Skew-t Distributions
snow Simple Network of Workstations
snowfall Easier cluster computing (based on snow).
softImpute Matrix Completion via Iterative Soft-Thresholded SVD
sourcetools Tools for Reading, Tokenizing and Parsing R Code
sp Classes and Methods for Spatial Data
spam SPArse Matrix
SparseM Sparse Linear Algebra
spatial Functions for Kriging and Point Pattern Analysis
spdep Spatial Dependence: Weighting Schemes, Statistics and Models
splines Regression Spline Functions and Classes
stabledist Stable Distribution Functions
StanHeaders C++ Header Files for Stan
statmod Statistical Modeling
stats The R Stats Package
stats4 Statistical Functions using S4 Classes
stringdist Approximate String Matching and String Distance Functions
stringi Character String Processing Facilities
stringr Simple, Consistent Wrappers for Common String Operations
SummarizedExperiment SummarizedExperiment container
survey Analysis of Complex Survey Samples
survival Survival Analysis
sva Surrogate Variable Analysis
tcltk Tcl/Tk Interface
testthat Unit Testing for R
tgp Bayesian Treed Gaussian Process Models
TH.data TH's Data Archive
threejs Interactive 3D Scatter Plots, Networks and Globes
tibble Simple Data Frames
tidyr Easily Tidy Data with spread() and gather() Functions
tkrplot TK Rplot
tools Tools for Package Development
trimcluster Cluster analysis with trimming
truncnorm Truncated normal distribution
tseries Time Series Analysis and Computational Finance
TxDb.Hsapiens.UCSC.hg19.knownGene Annotation package for TxDb object(s)
utils The R Utils Package
VariantAnnotation Annotation of Genetic Variants
vegan Community Ecology Package
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
wateRmelon Illumina 450 methylation array normalization and metrics
WGCNA Weighted Correlation Network Analysis
whisker for R, logicless templating
widgetTools Creates an interactive tcltk widget
XML Tools for Parsing and Generating XML Within R and S-Plus
xps Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
xtable Export Tables to LaTeX or HTML
xts eXtensible Time Series
XVector Representation and manpulation of external sequences
yaml Methods to Convert R Data to YAML and Back
zlibbioc An R packaged zlib-1.2.5
zoo S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)