# R and Bioconductor Packages installed on RC Systemsยง

Note

Please consider replacing this with instructions on how to retrieve this list, instead of the list itself.

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) |