R
Contents
Description
R is a free software environment for statistical computing and graphics.
Note: File a support ticket to request installation of additional libraries.
Required Modules
Serial
- R
Parallel (MPI)
- Rmpi
The "Rmpi" module enables access to the version of R that provides the Rmpi library for large-scale multi-node parallel computations.
See Rmpi documentation for details.
System Variables
- HPC_R_DIR - installation directory
- HPC_R_BIN - executable directory
- HPC_R_LIB - library directory
- HPC_R_INCLUDE - includes directory
How To Run
R can be run on the command-line (or the batch system) using the 'Rscript myscript.R
' or 'R CMD BATCH myscript.R
' command. For script development or visualization RStudio GUI application can be used. See the respective documentation for details. For RStudio, load the following modules within your job script before running the rstudio command:
module load gui rstudio
- Notes and Warnings
- Java
rJava users need to load the java module manually with 'module load java/1.7.0_79
'
- TMPDIR
If temporary files are produced the may fill up memory disks on HPG2 nodes and cause node and job failures. Use something like
mkdir -p tmp export TMPDIR=$(pwd)/tmp
in your job script to prevent this and launch your job from the respective directory and not from your home directory.
- Tasks vs Cores for parallel runs
Parallel threads in an R job will be bound to the same CPU core even if multiple ntasks are specified in the job script. Use cpus-per-task to use R 'parallel' module correctly. For example, for an 8-thread parallel job use the following resource request in your job script:
#SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=8
See the single-threaded and multi-threaded examples on the Sample SLURM Scripts page for more details.
Performance
We have benchmarked our most recent installed R version (3.0.2) built with the included blas/lapack libraries versus the newest (as of April 2015) release 3.2.0 built with Intel MKL libraries on the HiPerGator1 hardware (AMD Abu Dhabi 2.4GHz CPUs) and the Intel Haswell 2.3GHz CPUs we're testing for possible usage in HiPerGator2. The results are presented in the R Benchmark 2.5 table
FAQ
- Q: When I submit a job using 'parallel' package all threads seem to share a single CPU core instead of running on the separate cores I requested.
- A: On SLURM you need to use --cpus-per-task to specify the number of available cores. E.g.
#SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --cpus-per-task=12
will allow mcapply or other function from the 'parallel' package to run on all requested cores
Rmpi Example
See R MPI Example page for an example of using Rmpi code.
Installed Libraries
Note: Many of the packages in the R library shown below are installed as a part of Bioconductor meta-library. The list is generated from the default R version.
Name | Description |
---|---|
a4Base | Automated Affymetrix Array Analysis Base Package |
a4Classif | Automated Affymetrix Array Analysis Classification Package |
a4Core | Automated Affymetrix Array Analysis Core Package |
a4Preproc | Automated Affymetrix Array Analysis Preprocessing Package |
a4Reporting | Automated Affymetrix Array Analysis Reporting Package |
abc | Tools for Approximate Bayesian Computation (ABC) |
abc.data | Data Only: Tools for Approximate Bayesian Computation (ABC) |
abind | Combine Multidimensional Arrays |
acepack | ace() and avas() for selecting regression transformations |
aCGH | Classes and functions for Array Comparative Genomic Hybridization data. |
actuar | Actuarial Functions and Heavy Tailed Distributions |
ade4 | Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences |
afex | Analysis of Factorial Experiments |
affxparser | Affymetrix File Parsing SDK |
affy | Methods for Affymetrix Oligonucleotide Arrays |
affydata | Affymetrix Data for Demonstration Purpose |
affyio | Tools for parsing Affymetrix data files |
affyPLM | Methods for fitting probe-level models |
affyQCReport | QC Report Generation for affyBatch objects |
AGDEX | Agreement of Differential Expression Analysis |
Agi4x44PreProcess | PreProcessing of Agilent 4x44 array data |
agricolae | Statistical Procedures for Agricultural Research |
akima | Interpolation of Irregularly and Regularly Spaced Data |
AlgDesign | Algorithmic Experimental Design |
animation | A Gallery of Animations in Statistics and Utilities to Create Animations |
annaffy | Annotation tools for Affymetrix biological metadata |
AnnBuilder | Bioconductor annotation data package builder |
annotate | Annotation for microarrays |
AnnotationDbi | Annotation Database Interface |
AnnotationForge | Code for Building Annotation Database Packages |
aod | Analysis of Overdispersed Data |
ape | Analyses of Phylogenetics and Evolution |
aplpack | Another Plot PACKage: stem.leaf |
arm | Data Analysis Using Regression and Multilevel/Hierarchical Models |
aroma.affymetrix | Analysis of Large Affymetrix Microarray Data Sets |
aroma.apd | A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated] |
aroma.core | Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework |
aroma.light | Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types |
arrayQualityMetrics | Quality metrics report for microarray data sets |
asremlPlus | Augments the Use of 'Asreml' in Fitting Mixed Models |
assertthat | Easy pre and post assertions. |
aster | Aster Models |
auteur | Bayesian sampler of the trait-evolutionary process |
auto3dgm | 3-Dimensional Geometric Morphometrics |
automap | Automatic interpolation package |
aws | Adaptive Weights Smoothing |
awsMethods | Class and Methods Definitions for Packages 'aws' |
BAMD | Bayesian Association Model for Genomic Data with Missing Covariates |
base64 | Base64 Encoder and Decoder |
base64enc | Tools for base64 encoding |
baseline | Baseline Correction of Spectra |
batchmeans | Consistent Batch Means Estimation of Monte Carlo Standard Errors |
batman | Bayesian AuTomated Metabolite Analyser for NMR spectra |
BayesLogit | Logistic Regression |
BayesTree | Bayesian Additive Regression Trees |
baySeq | Empirical Bayesian analysis of patterns of differential expression in count data |
BB | Solving and Optimizing Large-Scale Nonlinear Systems |
bdsmatrix | Routines for Block Diagonal Symmetric matrices |
beadarray | Quality assessment and low-level analysis for Illumina BeadArray data |
BeadDataPackR | Compression of Illumina BeadArray data |
beanplot | Visualization via Beanplots (like Boxplot/Stripchart/Violin Plot) |
Benchmarking | Benchmark and Frontier Analysis Using DEA and SFA |
bfast | Breaks For Additive Season and Trend (BFAST) |
BGLR | Bayesian Generalized Linear Regression |
BH | Boost C++ Header Files |
BiasedUrn | Biased Urn Model Distributions |
BigVAR | Dimension Reduction Methods for Multivariate Time Series |
binom | Binomial Confidence Intervals For Several Parameterizations |
Biobase | Biobase: Base functions for Bioconductor |
BiocGenerics | S4 generic functions for Bioconductor |
BiocInstaller | Install/Update Bioconductor |
BiocParallel | Bioconductor facilities for parallel evaluation |
BioGeoBEARS | BioGeography with Bayesian (and Likelihood) Evolutionary Analysis in R Scripts |
biom | An interface package (beta) for the BIOM file format. |
biomaRt | Interface to BioMart databases (e.g. Ensembl |
biomod2 | Ensemble platform for species distribution modeling |
BIOM.utils | Utilities for the BIOM (Biological Observation Matrix) Format |
Biostrings | String objects representing biological sequences |
biovizBase | Basic graphic utilities for visualization of genomic data. |
bit | A class for vectors of 1-bit booleans |
bitops | Bitwise Operations |
biwt | Functions to compute the biweight mean vector and covariance & correlation matrices |
blockmodeling | An R package for Generalized and classical blockmodeling of valued networks |
BLR | Bayesian Linear Regression |
bold | Interface to Bold Systems 'API' |
brew | Templating Framework for Report Generation |
BSgenome | Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation |
BSgenome.Hsapiens.UCSC.hg19 | Full genome sequences for Homo sapiens (UCSC version hg19) |
bumphunter | Bump Hunter |
Cairo | R graphics device using cairo graphics library for creating high-quality bitmap (PNG |
cairoDevice | Cairo-based Graphics Device Driver |
calibrate | Calibration of Scatterplot and Biplot Axes |
camel | Calibrated Machine Learning |
CAMERA | Collection of annotation related methods for mass spectrometry data |
caper | Comparative Analyses of Phylogenetics and Evolution in R |
car | Companion to Applied Regression |
caret | Classification and Regression Training |
Category | Category Analysis |
caTools | Tools: moving window statistics |
CCA | Canonical correlation analysis |
cghFLasso | Detecting hot spot on CGH array data with fused lasso regression. |
chron | Chronological Objects which can Handle Dates and Times |
Ckmeans.1d.dp | Optimal and Fast Univariate k-Means Clustering |
cladoRcpp | C++ implementations of phylogenetic cladogenesis calculations |
clime | Constrained L1-minimization for Inverse (covariance) Matrix Estimation |
clue | Cluster Ensembles |
cluster | Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al. |
clusterGeneration | Random Cluster Generation (with Specified Degree of Separation) |
CNVtools | A package to test genetic association with CNV data |
coda | Output Analysis and Diagnostics for MCMC |
coin | Conditional Inference Procedures in a Permutation Test Framework |
colorspace | Color Space Manipulation |
combinat | combinatorics utilities |
CompQuadForm | Distribution function of quadratic forms in normal variables |
CompRandFld | Composite-Likelihood Based Analysis of Random Fields |
corHMM | Analysis of Binary Character Evolution |
cor.pairwise.tg | This package is to do correlation analysis in pairwise for all input samples |
corpcor | Efficient Estimation of Covariance and (Partial) Correlation |
coxme | Mixed Effects Cox Models |
CpGassoc | Association Between Methylation and a Phenotype of Interest |
crayon | Colored Terminal Output |
crlmm | Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays. |
CSAR | Statistical tools for the analysis of ChIP-seq data |
cubature | Adaptive multivariate integration over hypercubes |
cummeRbund | Analysis |
curl | A Modern and Flexible Web Client for R |
d3Network | Tools for creating D3 JavaScript network |
D3TableFilter | A table widget based on D3.js and the "HTML Table Filter Generator" |
dae | Functions Useful in the Design and ANOVA of Experiments |
data.table | Extension of Data.frame |
DBI | R Database Interface |
deldir | Delaunay Triangulation and Dirichlet (Voronoi) Tessellation |
DEoptimR | Differential Evolution Optimization in Pure R |
DESeq | Differential gene expression analysis based on the negative binomial distribution |
DESeq2 | Differential gene expression analysis based on the negative binomial distribution |
deSolve | Solvers for Initial Value Problems of Differential Equations (ODE |
devtools | Tools to Make Developing R Packages Easier |
DEXSeq | Inference of differential exon usage in RNA-Seq |
dfoptim | Derivative-Free Optimization |
DiagrammeR | Create Graph Diagrams and Flowcharts Using R |
DiceKriging | Kriging Methods for Computer Experiments |
dichromat | Color Schemes for Dichromats |
digest | Create Compact Hash Digests of R Objects |
diptest | Hartigan's Dip Test Statistic for Unimodality - Corrected |
dismo | Species Distribution Modeling |
distillery | Method Functions for Confidence Intervals and to Distill Information from an Object |
diversitree | Comparative Phylogenetic Analyses of Diversification |
diveRsity | A Comprehensive |
dlm | Bayesian and Likelihood Analysis of Dynamic Linear Models |
DNAcopy | DNA copy number data analysis |
doBy | Groupwise Statistics |
doMC | Foreach Parallel Adaptor for 'parallel' |
doParallel | Foreach Parallel Adaptor for the 'parallel' Package |
doRNG | Generic Reproducible Parallel Backend for foreach Loops |
doSNOW | Foreach Parallel Adaptor for the 'snow' Package |
dplyr | A Grammar of Data Manipulation |
dse | Dynamic Systems Estimation (Time Series Package) |
DT | A Wrapper of the JavaScript Library 'DataTables' |
dummies | Create dummy/indicator variables flexibly and efficiently |
dygraphs | Interface to 'Dygraphs' Interactive Time Series Charting Library |
dynamicTreeCut | Methods for Detection of Clusters in Hierarchical Clustering Dendrograms |
DynDoc | Dynamic document tools |
e1071 | Misc Functions of the Department of Statistics |
easyGgplot2 | Perform and customize easily a plot with ggplot2 |
EBSeq | An R package for gene and isoform differential expression analysis of RNA-seq data |
EDASeq | Exploratory Data Analysis and Normalization for RNA-Seq |
edgeR | Empirical analysis of digital gene expression data in R |
eeptools | Convenience Functions for Education Data |
effects | Effect Displays for Linear |
eiPack | eiPack: Ecological Inference and Higher-Dimension Data Management |
eiPackP | eiPackP: Ecological Inference and Higher-Dimension Data Management |
ellipse | Functions for drawing ellipses and ellipse-like confidence regions |
elrm | Exact Logistic Regression via MCMC |
EMMIXskew | The EM Algorithm and Skew Mixture Distribution |
emplik | Empirical Likelihood Ratio for Censored/Truncated Data |
emulator | Bayesian emulation of computer programs |
ENMeval | Automated Runs and Evaluations of Ecological Niche Models |
ENmix | Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip |
equate | Observed-Score Linking and Equating |
eRm | Extended Rasch Modeling |
estimability | Tools for Assessing Estimability of Linear Predictions |
evaluate | Parsing and Evaluation Tools that Provide More Details than the Default |
expm | Matrix Exponential |
expr.diff.ebseq.tg | this package to do differential gene expression analysis on two conditions. |
extRemes | Extreme Value Analysis |
FactoMineR | Multivariate Exploratory Data Analysis and Data Mining |
fastcluster | Fast Hierarchical Clustering Routines for R and Python |
fastmatch | Fast match() function |
fBasics | Rmetrics - Markets and Basic Statistics |
FD | Measuring functional diversity (FD) from multiple traits |
fda | Functional Data Analysis |
FDb.InfiniumMethylation.hg19 | Annotation package for Illumina Infinium DNA methylation probes |
fdrtool | Estimation of (Local) False Discovery Rates and Higher Criticism |
ff | memory-efficient storage of large data on disk and fast access functions |
ffbase | Basic Statistical Functions for Package 'ff' |
fGarch | Rmetrics - Autoregressive Conditional Heteroskedastic Modelling |
fields | Tools for Spatial Data |
FinTS | Companion to Tsay (2005) Analysis of Financial Time Series |
flashClust | Implementation of optimal hierarchical clustering |
flexmix | Flexible Mixture Modeling |
FNN | Fast Nearest Neighbor Search Algorithms and Applications |
foreach | Provides Foreach Looping Construct for R |
forecast | Forecasting Functions for Time Series and Linear Models |
formatR | Format R Code Automatically |
Formula | Extended Model Formulas |
fpc | Flexible Procedures for Clustering |
fracdiff | Fractionally differenced ARIMA aka ARFIMA(p |
fUnitRoots | Trends and Unit Roots |
futile.logger | A Logging Utility for R |
futile.options | Futile options management |
future | A Future API for R |
GA | Genetic Algorithms |
GAabbreviate | Abbreviating Items Measures using Genetic Algorithms |
gage | Generally Applicable Gene-set Enrichment for Pathway Analysis |
gageData | Auxillary data for gage package |
gam | Generalized Additive Models |
gamm4 | Generalized additive mixed models using mgcv and lme4 |
gbm | Generalized Boosted Regression Models |
gcrma | Background Adjustment Using Sequence Information |
gdata | Various R Programming Tools for Data Manipulation |
gdsfmt | R Interface to CoreArray Genomic Data Structure (GDS) Files |
gee | Generalized Estimation Equation Solver |
geepack | Generalized Estimating Equation Package |
geiger | Analysis of Evolutionary Diversification |
GenABEL | genome-wide SNP association analysis |
GenABEL.data | Package contains data which is used by GenABEL example and test functions |
GeneCycle | Identification of Periodically Expressed Genes |
genefilter | genefilter: methods for filtering genes from high-throughput experiments |
GeneNet | Modeling and Inferring Gene Networks |
geneplotter | Graphics related functions for Bioconductor |
genetics | Population Genetics |
GeneticsPed | Pedigree and genetic relationship functions |
genlasso | Path algorithm for generalized lasso problems |
GenomeInfoDb | Utilities for manipulating chromosome and other 'seqname' identifiers |
GenometriCorr | Genometric Correlation package |
GenomicAlignments | Representation and manipulation of short genomic alignments |
GenomicFeatures | Tools for making and manipulating transcript centric annotations |
GenomicRanges | Representation and manipulation of genomic intervals and variables defined along a genome |
GenSA | R Functions for Generalized Simulated Annealing |
geometry | Mesh Generation and Surface Tesselation |
GEOquery | Get data from NCBI Gene Expression Omnibus (GEO) |
geoR | Analysis of Geostatistical Data |
geoRglm | A Package for Generalised Linear Spatial Models |
geosphere | Spherical Trigonometry |
getopt | C-like getopt behavior. |
GGally | Extension to ggplot2 |
ggm | Functions for graphical Markov models |
ggmap | Spatial Visualization with ggplot2 |
ggplot2 | An Implementation of the Grammar of Graphics |
ggRandomForests | Visually Exploring Random Forests |
ggvis | Interactive Grammar of Graphics |
GIGrvg | Random Variate Generator for the GIG Distribution |
git2r | Provides Access to Git Repositories |
GLAD | Gain and Loss Analysis of DNA |
glasso | Graphical lasso- estimation of Gaussian graphical models |
glmmADMB | Generalized Linear Mixed Models using 'AD Model Builder' |
glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models |
globals | Identify Global Objects in R Expressions |
gmm | Generalized Method of Moments and Generalized Empirical Likelihood |
gmodels | Various R Programming Tools for Model Fitting |
gmp | Multiple Precision Arithmetic |
GO.db | A set of annotation maps describing the entire Gene Ontology |
goftest | Classical Goodness-of-Fit Tests for Univariate Distributions |
GOstats | Tools for manipulating GO and microarrays. |
GPfit | Gaussian Processes Modeling |
gplots | Various R Programming Tools for Plotting Data |
GPseq | gpseq: Using the generalized Poisson distribution to model sequence read counts from high throughput sequencing experiments |
graph | graph: A package to handle graph data structures |
gregmisc | Greg's Miscellaneous Functions |
gridBase | Integration of base and grid graphics |
gridExtra | Miscellaneous Functions for "Grid" Graphics |
gridSVG | Export 'grid' Graphics as SVG |
grofit | The package was developed to fit fit many growth curves obtained under different conditions. |
GSA | Gene set analysis |
gsalib | Utility Functions For GATK |
gsDesign | Group Sequential Design |
GSEABase | Gene set enrichment data structures and methods |
gsl | wrapper for the Gnu Scientific Library |
gsmoothr | Smoothing tools |
gss | General Smoothing Splines |
gstat | Spatial and Spatio-Temporal Geostatistical Modelling |
gsubfn | Utilities for strings and function arguments. |
gtable | Arrange 'Grobs' in Tables |
gtools | Various R Programming Tools |
Gviz | Plotting data and annotation information along genomic coordinates |
gWidgets | gWidgets API for building toolkit-independent |
gWidgetsRGtk2 | Toolkit implementation of gWidgets for RGtk2 |
HaploSim | Functions to simulate haplotypes |
haplo.stats | Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous |
heatmap.plus | Heatmap with more sensible behavior. |
hexbin | Hexagonal Binning Routines |
hglm | Hierarchical Generalized Linear Models |
hglm.data | Data for The hglm Package |
hgu133plus2.db | Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) |
hgu95av2.db | Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) |
hierNet | A Lasso for Hierarchical Interactions |
highr | Syntax Highlighting for R Source Code |
HilbertVis | Hilbert curve visualization |
hisse | Hidden State Speciation and Extinction |
Hmisc | Harrell Miscellaneous |
HSAUR2 | A Handbook of Statistical Analyses Using R (2nd Edition) |
htmltools | Tools for HTML |
htmlwidgets | HTML Widgets for R |
httpuv | HTTP and WebSocket Server Library |
httr | Tools for Working with URLs and HTTP |
huge | High-Dimensional Undirected Graph Estimation |
hwriter | HTML Writer - Outputs R objects in HTML format |
hydroGOF | Goodness-of-fit functions for comparison of simulated and observed hydrological time series |
hydroTSM | Time series management |
hyperSpec | Work with Hyperspectral Data |
Icens | NPMLE for Censored and Truncated Data |
ICS | Tools for Exploring Multivariate Data via ICS/ICA |
ICSNP | Tools for Multivariate Nonparametrics |
igraph | Network Analysis and Visualization |
IlluminaHumanMethylation450kanno.ilmn12.hg19 | Annotation for Illumina's 450k methylation arrays |
IlluminaHumanMethylation450kmanifest | Annotation for Illumina's 450k methylation arrays |
illuminaio | Parsing Illumina Microarray Output Files |
impute | impute: Imputation for microarray data |
in2extRemes | Into the extRemes Package |
INLA | Functions which Allow to Perform Full Bayesian Analysis of Latent Gaussian Models using Integrated Nested Laplace Approximations |
inline | Functions to Inline C |
interactiveDisplay | Package for enabling powerful shiny web displays of Bioconductor objects |
interactiveDisplayBase | Base package for enabling powerful shiny web displays of Bioconductor objects |
intergraph | Coercion Routines for Network Data Objects |
intervals | Tools for Working with Points and Intervals |
IRanges | Infrastructure for manipulating intervals on sequences |
irlba | Fast Truncated SVD |
iterators | Provides Iterator Construct for R |
itertools | Iterator Tools |
jpeg | Read and write JPEG images |
jsonlite | A Robust |
KEGG.db | A set of annotation maps for KEGG |
KEGGgraph | KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor |
KEGGREST | Client-side REST access to KEGG |
kernlab | Kernel-Based Machine Learning Lab |
KFAS | Kalman Filter and Smoother for Exponential Family State Space Models |
klaR | Classification and visualization |
knitr | A General-Purpose Package for Dynamic Report Generation in R |
ks | Kernel Smoothing |
labeling | Axis Labeling |
lambda.r | Modeling Data with Functional Programming |
lars | Least Angle Regression |
laser | Likelihood Analysis of Speciation/Extinction Rates from Phylogenies |
lassoshooting | L1 regularized regression (Lasso) solver using the Cyclic Coordinate Descent algorithm aka Lasso Shooting |
lattice | Trellis Graphics for R |
latticeExtra | Extra Graphical Utilities Based on Lattice |
lavaan | Latent Variable Analysis |
lazyeval | Lazy (Non-Standard) Evaluation |
LDcorSV | Linkage disequilibrium corrected by the structure and the relatedness |
LDna | Linkage disequilibrum network analysis (LDna) |
LEA | LEA: an R package for Landscape and Ecological Association Studies |
leaps | regression subset selection |
LearnBayes | Functions for Learning Bayesian Inference |
lhs | Latin Hypercube Samples |
limma | Linear Models for Microarray Data |
limSolve | Solving Linear Inverse Models |
linprog | Linear Programming / Optimization |
listenv | Environments Behaving (Almost) as Lists |
lme4 | Linear Mixed-Effects Models using 'Eigen' and S4 |
lmomco | L-Moments |
Lmoments | L-Moments and Quantile Mixtures |
lmtest | Testing Linear Regression Models |
locfit | Local Regression |
longitudinal | Analysis of Multiple Time Course Data |
loo | Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models |
LPCM | Local Principal Curve Methods |
lpridge | Local Polynomial (Ridge) Regression |
lpSolve | Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs |
lpSolveAPI | R Interface to 'lp_solve' Version 5.5.2.0 |
lsa | Latent Semantic Analysis |
lsmeans | Least-Squares Means |
ltm | Latent Trait Models under IRT |
lubridate | Make Dealing with Dates a Little Easier |
lumi | BeadArray Specific Methods for Illumina Methylation and Expression Microarrays |
maanova | Tools for analyzing Micro Array experiments |
magic | create and investigate magic squares |
magrittr | A Forward-Pipe Operator for R |
manipulate | Interactive Plots for RStudio |
mapdata | Extra Map Databases |
mapproj | Map Projections |
maps | Draw Geographical Maps |
maptools | Tools for Reading and Handling Spatial Objects |
markdown | 'Markdown' Rendering for R |
marray | Exploratory analysis for two-color spotted microarray data |
MARSS | Multivariate Autoregressive State-Space Modeling |
MASS | Support Functions and Datasets for Venables and Ripley's MASS |
MatchingFrontier | Computation of the Balance - Sample Size Frontier in Matching Methods for Causal Inference |
MatchIt | MatchIt: Nonparametric Preprocessing for Parametric Casual Inference |
matR | Metagenomics Analysis Tools for R |
Matrix | Sparse and Dense Matrix Classes and Methods |
matrixcalc | Collection of functions for matrix calculations |
MatrixEQTL | Matrix eQTL: Ultra fast eQTL analysis via large matrix operations |
MatrixModels | Modelling with Sparse And Dense Matrices |
matrixStats | Functions that Apply to Rows and Columns of Matrices (and to Vectors) |
MaxentVariableSelection | Selecting the Best Set of Relevant Environmental Variables along with the Optimal Regularization Multiplier for Maxent Niche Modeling |
mboost | Model-Based Boosting |
mclust | Gaussian Mixture Modelling for Model-Based Clustering |
mcmc | Markov Chain Monte Carlo |
MCMCglmm | MCMC Generalised Linear Mixed Models |
MCMCpack | Markov chain Monte Carlo (MCMC) Package |
mda | Mixture and Flexible Discriminant Analysis |
memisc | Tools for Management of Survey Data and the Presentation of Analysis Results |
memoise | Memoisation of Functions |
metagenomeSeq | Statistical analysis for sparse high-throughput sequencing |
methylumi | Handle Illumina methylation data |
MetStaT | Statistical metabolomics tools |
MGRASTer | API Client for the MG-RAST Server of the US DOE KBase |
mi | Missing Data Imputation and Model Checking |
microbenchmark | Accurate Timing Functions |
mime | Map Filenames to MIME Types |
minerva | Maximal Information-Based Nonparametric Exploration R Package for Variable Analysis |
minfi | Analyze Illumina's 450k methylation arrays |
minqa | Derivative-free optimization algorithms by quadratic approximation |
misc3d | Miscellaneous 3D Plots |
missMethyl | Analysis of methylation array data |
mitools | Tools for multiple imputation of missing data |
mixOmics | Omics Data Integration Project |
mlbench | Machine Learning Benchmark Problems |
mlegp | Maximum Likelihood Estimates of Gaussian Processes |
MLInterfaces | Uniform interfaces to R machine learning procedures for data in Bioconductor containers |
mmap | Map Pages of Memory |
mnormt | The Multivariate Normal and t Distributions |
modeltools | Tools and Classes for Statistical Models |
mombf | Moment and Inverse Moment Bayes Factors |
monomvn | Estimation for Multivariate Normal and Student-t Data with Monotone Missingness |
mpm | Multivariate Projection Methods |
msdata | Various Mass Spectrometry raw data example files |
msm | Multi-State Markov and Hidden Markov Models in Continuous Time |
MTS | All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS) and Estimating Multivariate Volatility Models |
multcomp | Simultaneous Inference in General Parametric Models |
multicool | Permutations of Multisets in Cool-Lex Order |
multiwayvcov | Multi-Way Standard Error Clustering |
multtest | Resampling-based multiple hypothesis testing |
munsell | Utilities for Using Munsell Colours |
MVA | An Introduction to Applied Multivariate Analysis with R |
mvtnorm | Multivariate Normal and t Distributions |
mzR | parser for netCDF |
NarrowPeaks | Shape-based Analysis of Variation in ChIP-seq using Functional PCA |
ncbit | retrieve and build NBCI taxonomic data |
ncdf | Interface to Unidata netCDF Data Files |
ncvreg | Regularization Paths for SCAD and MCP Penalized Regression Models |
neldermead | R port of the Scilab neldermead module |
network | Classes for Relational Data |
ngspatial | Fitting the centered autologistic and sparse spatial generalized linear mixed models for areal data |
nleqslv | Solve Systems of Nonlinear Equations |
nlme | Linear and Nonlinear Mixed Effects Models |
nloptr | R interface to NLopt |
NLP | Natural Language Processing Infrastructure |
nls2 | Non-linear regression with brute force |
NMF | Algorithms and Framework for Nonnegative Matrix Factorization (NMF) |
nnls | The Lawson-Hanson algorithm for non-negative least squares (NNLS) |
NOISeq | Exploratory analysis and differential expression for RNA-seq data |
nonrandom | Stratification and matching by the propensity score |
nor1mix | Normal (1-d) Mixture Models (S3 Classes and Methods) |
numDeriv | Accurate Numerical Derivatives |
oligo | Preprocessing tools for oligonucleotide arrays |
oligoClasses | Classes for high-throughput arrays supported by oligo and crlmm |
openssl | Toolkit for Encryption |
openxlsx | Read |
optextras | Tools to Support Optimization Methods |
optimbase | R port of the Scilab optimbase module |
optimsimplex | R port of the Scilab optimsimplex module |
optimx | A Replacement and Extension of the optim() Function |
optparse | Command Line Option Parser |
org.Hs.eg.db | Genome wide annotation for Human |
org.Mm.eg.db | Genome wide annotation for Mouse |
ouch | Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses |
outliers | Tests for outliers |
OUwie | Analysis of Evolutionary Rates in an OU Framework |
packrat | A Dependency Management System for Projects and their R Package Dependencies |
pamr | Pam: prediction analysis for microarrays |
ParallelStructure | function to run parallel jobs in STRUCTURE |
parmigene | Parallel Mutual Information estimation for Gene Network reconstruction. |
party | A Laboratory for Recursive Partytioning |
pastis | Phylogenetic Assembly with Soft Taxonomic Inferences |
pathview | a tool set for pathway based data integration and visualization |
pbivnorm | Vectorized Bivariate Normal CDF |
pbkrtest | Parametric Bootstrap and Kenward-Roger-Based Methods for Mixed Model Comparison |
pcaPP | Robust PCA by Projection Pursuit |
pd.aragene.1.1.st | Platform Design Info for Affymetrix AraGene-1_1-st |
pd.huex.1.0.st.v2 | Platform Design Info for Affymetrix HuEx-1_0-st-v2 |
pedigree | Pedigree functions |
pedigreemm | Pedigree-based mixed-effects models |
peer | PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. |
perm | Exact or Asymptotic permutation tests |
permute | Functions for Generating Restricted Permutations of Data |
phangorn | Phylogenetic Analysis in R |
pheatmap | Pretty Heatmaps |
phia | Post-Hoc Interaction Analysis |
phybase | Basic functions for phylogenetic analysis |
phyext | An extension of some of the classes in phylobase. Tree objects now support subnodes on branches |
phylobase | Base Package for Phylogenetic Structures and Comparative Data |
phyloseq | Handling and analysis of high-throughput microbiome census data |
phytools | Phylogenetic Tools for Comparative Biology (and Other Things) |
picante | R tools for integrating phylogenies and ecology |
pixmap | Bitmap Images (``Pixel Maps) |
pkgmaker | Package development utilities |
PKI | Public Key Infrastucture for R Based on the X.509 Standard |
plier | Implements the Affymetrix PLIER algorithm |
plotrix | Various Plotting Functions |
pls | Partial Least Squares and Principal Component Regression |
plyr | Tools for Splitting |
png | Read and write PNG images |
polspline | Polynomial Spline Routines |
polyclip | Polygon Clipping |
polycor | Polychoric and Polyserial Correlations |
pomp | Statistical Inference for Partially Observed Markov Processes |
PopGenome | An Efficient Swiss Army Knife for Population Genomic Analyses |
prabclus | Functions for Clustering of Presence-Absence |
praise | Praise Users |
preprocessCore | A collection of pre-processing functions |
prettyR | Pretty Descriptive Stats |
pROC | Display and Analyze ROC Curves |
PROcess | Ciphergen SELDI-TOF Processing |
proftools | Profile Output Processing Tools for R |
proj4 | A simple interface to the PROJ.4 cartographic projections library |
ProtGenerics | S4 generic functions for Bioconductor proteomics infrastructure |
proto | Prototype object-based programming |
pryr | Tools for Computing on the Language |
PSCBS | Analysis of Parent-Specific DNA Copy Numbers |
pscl | Political Science Computational Laboratory |
psiplot | Generate plots of PSI values generated by vast-tools |
psych | Procedures for Psychological |
ptw | Parametric Time Warping |
pvclust | Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling |
qgraph | Graph Plotting Methods |
qqman | Q-Q and manhattan plots for GWAS data |
qtl | Tools for Analyzing QTL Experiments |
quadprog | Functions to solve Quadratic Programming Problems. |
quantreg | Quantile Regression |
qvalue | Q-value estimation for false discovery rate control |
R2admb | 'ADMB' to R Interface Functions |
R2jags | Using R to Run 'JAGS' |
R2WinBUGS | Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS' |
R6 | Classes with Reference Semantics |
RandomFields | Simulation and Analysis of Random Fields |
RandomFieldsUtils | Utilities for the Simulation and Analysis of Random Fields |
randomForest | Breiman and Cutler's Random Forests for Classification and Regression |
randomForestSRC | Random Forests for Survival |
RankProd | Rank Product method for identifying differentially expressed genes with application in meta-analysis |
raster | Geographic Data Analysis and Modeling |
rasterVis | Visualization Methods for Raster Data |
RBGL | An interface to the BOOST graph library |
R.cache | Fast and Light-Weight Caching (Memoization) of Objects and Results to Speed Up Computations |
Rcgmin | Conjugate Gradient Minimization of Nonlinear Functions |
Rcmdr | R Commander |
RcmdrMisc | R Commander Miscellaneous Functions |
RColorBrewer | ColorBrewer Palettes |
Rcpp | Seamless R and C++ Integration |
RcppArmadillo | 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra Library |
RcppEigen | 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library |
RcppParallel | Parallel Programming Tools for 'Rcpp' |
RCurl | General Network (HTTP/FTP/...) Client Interface for R |
rda | Shrunken Centroids Regularized Discriminant Analysis |
R.devices | Unified Handling of Graphics Devices |
readr | Read Tabular Data |
readstata13 | Import Stata Data Files |
readxl | Read Excel Files |
registry | Infrastructure for R Package Registries |
relaimpo | Relative importance of regressors in linear models |
relimp | Relative Contribution of Effects in a Regression Model |
rentrez | Entrez in R |
RepeatABEL | GWAS for Multiple Observations on Related Individuals |
reshape | Flexibly reshape data. |
reshape2 | Flexibly Reshape Data: A Reboot of the Reshape Package. |
rexpokit | R wrappers for EXPOKIT; other matrix functions |
R.filesets | Easy Handling of and Access to Files Organized in Structured Directories |
rgdal | Bindings for the Geospatial Data Abstraction Library |
rgenoud | R Version of GENetic Optimization Using Derivatives |
rgeos | Interface to Geometry Engine - Open Source (GEOS) |
rgl | 3D Visualization Using OpenGL |
RgoogleMaps | Overlays on Google map tiles in R |
Rgraphviz | Provides plotting capabilities for R graph objects |
RGtk2 | R bindings for Gtk 2.8.0 and above |
R.huge | Methods for Accessing Huge Amounts of Data [deprecated] |
ridigbio | Interface to the iDigBio Data API |
Ringo | R Investigation of ChIP-chip Oligoarrays |
rjags | Bayesian Graphical Models using MCMC |
rJava | Low-Level R to Java Interface |
rjson | JSON for R |
RJSONIO | Serialize R objects to JSON |
Rlab | Functions and Datasets Required for ST370 class |
RMark | R Code for Mark Analysis |
rmarkdown | Dynamic Documents for R |
R.matlab | Read and Write MAT Files and Call MATLAB from Within R |
R.methodsS3 | S3 Methods Simplified |
RmiR.hsa | Various databases of microRNA Targets |
Rmisc | Rmisc: Ryan Miscellaneous |
Rmpfr | R MPFR - Multiple Precision Floating-Point Reliable |
rms | Regression Modeling Strategies |
RMySQL | Database Interface and 'MySQL' Driver for R |
rncl | An Interface to the Nexus Class Library |
RNetCDF | R Interface to NetCDF Datasets |
RNeXML | Semantically Rich I/O for the 'NeXML' Format |
rngtools | Utility functions for working with Random Number Generators |
robustbase | Basic Robust Statistics |
ROC | utilities for ROC |
ROCR | Visualizing the Performance of Scoring Classifiers |
R.oo | R Object-Oriented Programming with or without References |
rootSolve | Nonlinear Root Finding |
roxygen2 | In-Source Documentation for R |
rpanel | Simple interactive controls for R using the tcltk library. |
RPMM | Recursively Partitioned Mixture Model |
rrBLUP | Ridge Regression and Other Kernels for Genomic Selection |
rrcov | Scalable Robust Estimators with High Breakdown Point |
R.rsp | Dynamic Generation of Scientific Reports |
Rsamtools | Binary alignment (BAM) |
rsconnect | Deployment Interface for R Markdown Documents and Shiny Applications |
Rserve | Binary R server |
rsgcc | Gini methodology-based correlation and clustering analysis of microarray and RNA-Seq gene expression data |
Rsolnp | General Non-Linear Optimization |
RSQLite | SQLite Interface for R |
RSQLite.extfuns | Math and String Extension Functions for RSQLite |
Rssa | A Collection of Methods for Singular Spectrum Analysis |
rstan | R Interface to Stan |
rstudio | Tools and Utilities for RStudio |
rstudioapi | Safely Access the RStudio API |
Rsubread | Subread sequence alignment for R |
rtracklayer | R interface to genome browsers and their annotation tracks |
RUnit | R Unit Test Framework |
R.utils | Various Programming Utilities |
ruv | Detect and Remove Unwanted Variation using Negative Controls |
RUVSeq | Remove Unwanted Variation from RNA-Seq Data |
rversions | Query 'R' Versions |
rvest | Easily Harvest (Scrape) Web Pages |
Rvmmin | Variable Metric Nonlinear Function Minimization |
Rwave | Time-Frequency Analysis of 1-D Signals |
RWeka | R/Weka interface |
RWekajars | R/Weka interface jars |
S4Vectors | S4 implementation of vectors and lists |
sandwich | Robust Covariance Matrix Estimators |
scales | Scale Functions for Visualization |
scatterplot3d | 3D Scatter Plot |
scDD | Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions |
sealasso | Standard Error Adjusted Adaptive Lasso |
season | Seasonal analysis of health data |
segmented | Regression Models with Breakpoints/Changepoints Estimation |
selectr | Translate CSS Selectors to XPath Expressions |
sem | Structural Equation Models |
SemiPar | Semiparametic Regression |
seqinr | Biological Sequences Retrieval and Analysis |
seqLogo | Sequence logos for DNA sequence alignments |
seqMeta | Meta-Analysis of Region-Based Tests of Rare DNA Variants |
setRNG | Set (Normal) Random Number Generator and Seed |
sfsmisc | Utilities from "Seminar fuer Statistik" ETH Zurich |
SGL | Fit a GLM (or cox model) with a combination of lasso and group lasso regularization |
shapefiles | Read and Write ESRI Shapefiles |
shiny | Web Application Framework for R |
shinydashboard | Create Dashboards with 'Shiny' |
shinyjs | Perform Common JavaScript Operations in Shiny Apps using Plain R Code |
shinystan | Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models |
shinythemes | Themes for Shiny |
ShortRead | FASTQ input and manipulation |
siggenes | Multiple testing using SAM and Efron's empirical Bayes approaches |
simpleaffy | Very simple high level analysis of Affymetrix data |
SimRAD | Simulations to Predict the Number of RAD and GBS Loci |
simsem | SIMulated Structural Equation Modeling |
slam | Sparse Lightweight Arrays and Matrices |
sna | Tools for Social Network Analysis |
snow | Simple Network of Workstations |
SnowballC | Snowball stemmers based on the C libstemmer UTF-8 library |
snowfall | Easier cluster computing (based on snow). |
SNPassoc | SNPs-based whole genome association studies |
SNPchip | Visualizations for copy number alterations |
SNPRelate | Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data |
sp | Classes and Methods for Spatial Data |
spacetime | Classes and Methods for Spatio-Temporal Data |
spam | SPArse Matrix |
SparseM | Sparse Linear Algebra |
spatial.tools | R functions for working with spatial data. |
SpatioTemporal | Spatio-Temporal Model Estimation |
spatstat | Spatial Point Pattern Analysis |
spBayes | Univariate and Multivariate Spatial-temporal Modeling |
spdep | Spatial Dependence: Weighting Schemes |
SPEI | Calculation of the Standardised Precipitation-Evapotranspiration Index |
spgwr | Geographically Weighted Regression |
splancs | Spatial and Space-Time Point Pattern Analysis |
spTDyn | Spatially Varying and Spatio-Temporal Dynamic Linear Models |
sqldf | Perform SQL Selects on R Data Frames |
stabledist | Stable Distribution Functions |
stabs | Stability Selection with Error Control |
StanHeaders | C++ Header Files for Stan |
stargazer | Well-Formatted Regression and Summary Statistics Tables |
statmod | Statistical Modeling |
STITCH | STITCH - Sequencing To Imputation Through Constructing Haplotypes |
stringi | Character String Processing Facilities |
stringr | Simple |
strucchange | Testing |
subplex | Unconstrained Optimization using the Subplex Algorithm |
SummarizedExperiment | SummarizedExperiment container |
SuppDists | Supplementary Distributions |
survey | analysis of complex survey samples |
survival | Survival Analysis |
sva | Surrogate Variable Analysis |
svd | Interfaces to Various State-of-Art SVD and Eigensolvers |
SVGAnnotation | Tools for post-processing SVG plots created in R |
svUnit | SciViews GUI API - Unit testing |
tau | Text Analysis Utilities |
taxize | Taxonomic Information from Around the Web |
tcltk2 | Tcl/Tk Additions |
tensor | Tensor product of arrays |
tensorA | Advanced tensors arithmetic with named indices |
testthat | Unit Testing for R |
tfplot | Time Frame User Utilities |
tframe | Time Frame Coding Kernel |
TH.data | TH's Data Archive |
threejs | Interactive 3D Scatter Plots |
tibble | Simple Data Frames |
tidyr | Easily Tidy Data with `spread()` and `gather()` Functions |
tilingArray | Transcript mapping with high-density oligonucleotide tiling arrays |
timeDate | Rmetrics - Chronological and Calendar Objects |
timeSeries | Rmetrics - Financial Time Series Objects |
tm | Text Mining Package |
tmvtnorm | Truncated Multivariate Normal and Student t Distribution |
topGO | topGO: Enrichment analysis for Gene Ontology |
TreeSim | Simulating Phylogenetic Trees |
trimcluster | Cluster analysis with trimming |
truncnorm | Truncated normal distribution |
trust | Trust Region Optimization |
TSA | Time Series Analysis |
tseries | Time Series Analysis and Computational Finance |
tseriesChaos | Analysis of nonlinear time series |
tviz | Visualisation of gene and transcript expression levels from RNA-seq experiments |
TxDb.Hsapiens.UCSC.hg19.knownGene | Annotation package for TxDb object(s) |
ucminf | General-purpose unconstrained non-linear optimization |
unmarked | Models for Data from Unmarked Animals |
urca | Unit Root and Cointegration Tests for Time Series Data |
usdm | Uncertainty Analysis for Species Distribution Models |
uuid | Tools for generating and handling of UUIDs |
VariantAnnotation | Annotation of Genetic Variants |
vars | VAR Modelling |
varSelectIP | Objective Bayes Model Selection |
varSelRF | Variable Selection using Random Forests |
vcd | Visualizing Categorical Data |
vegan | Community Ecology Package |
VennDiagram | Generate High-Resolution Venn and Euler Plots |
VGAM | Vector Generalized Linear and Additive Models |
viridisLite | Default Color Maps from 'matplotlib' (Lite Version) |
visNetwork | Network Visualization using 'vis.js' Library |
vsn | Variance stabilization and calibration for microarray data |
wateRmelon | Illumina 450 methylation array normalization and metrics |
wavelets | A package of functions for computing wavelet filters |
waveslim | Basic wavelet routines for one- |
wavethresh | Wavelets statistics and transforms. |
WGCNA | Weighted Correlation Network Analysis |
WGDgc | Whole genome duplication detection using gene counts |
whisker | {{mustache}} for R |
withr | Run Code 'With' Temporarily Modified Global State |
wordcloud | Word Clouds |
xcms | LC/MS and GC/MS Data Analysis |
xlsx | Read |
xlsxjars | Package required POI jars for the xlsx package |
XML | Tools for Parsing and Generating XML Within R and S-Plus |
xml2 | Parse XML |
xpose4 | Tools for Nonlinear Mixed-Effect Model Building and Diagnostics |
xps | Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays |
xtable | Export Tables to LaTeX or HTML |
xts | eXtensible Time Series |
XVector | Representation and manpulation of external sequences |
yaml | Methods to convert R data to YAML and back |
zlibbioc | An R packaged zlib-1.2.5 |
zoo | S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations) |
base | The R Base Package |
boot | Bootstrap Functions (Originally by Angelo Canty for S) |
class | Functions for Classification |
cluster | Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al. |
codetools | Code Analysis Tools for R |
compiler | The R Compiler Package |
datasets | The R Datasets Package |
foreign | Read Data Stored by Minitab |
graphics | The R Graphics Package |
grDevices | The R Graphics Devices and Support for Colours and Fonts |
grid | The Grid Graphics Package |
KernSmooth | Functions for Kernel Smoothing Supporting Wand & Jones (1995) |
lattice | Trellis Graphics for R |
MASS | Support Functions and Datasets for Venables and Ripley's MASS |
Matrix | Sparse and Dense Matrix Classes and Methods |
methods | Formal Methods and Classes |
mgcv | Mixed GAM Computation Vehicle with GCV/AIC/REML Smoothness Estimation |
nlme | Linear and Nonlinear Mixed Effects Models |
nnet | Feed-Forward Neural Networks and Multinomial Log-Linear Models |
parallel | Support for Parallel computation in R |
rpart | Recursive Partitioning and Regression Trees |
spatial | Functions for Kriging and Point Pattern Analysis |
splines | Regression Spline Functions and Classes |
stats | The R Stats Package |
stats4 | Statistical Functions using S4 Classes |
survival | Survival Analysis |
tcltk | Tcl/Tk Interface |
tools | Tools for Package Development |
utils | The R Utils Package |