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<pre>
[[Category:Software]]
abind                  Combine multi-dimensional arrays
{{#get_file_data:file=R_PACKAGES
aCGH                    Classes and functions for Array Comparative
|data=name=Package,description=Title
                        Genomic Hybridization data.
|format=CSV with header
ade4                    Analysis of Ecological Data : Exploratory and
|cache seconds=3600
                        Euclidean methods in Environmental sciences
}}
affxparser              Affymetrix File Parsing SDK
{| class="wikitable"
affy                    Methods for Affymetrix Oligonucleotide Arrays
! Name
affydata                Affymetrix Data for Demonstration Purpose
! Description {{#for_external_table:<nowiki/>
affyio                  Tools for parsing Affymetrix data files
{{!}}-
affyPLM                Methods for fitting probe-level models
{{!}} {{{name}}}
affyQCReport            QC Report Generation for affyBatch objects
{{!}} {{{description}}}}}
Agi4x44PreProcess      PreProcessing of Agilent 4x44 array data
|}
agricolae              Statistical Procedures for Agricultural
                        Research
akima                  Interpolation of irregularly spaced data
annaffy                Annotation tools for Affymetrix biological
                        metadata
annotate                Annotation for microarrays
AnnotationDbi          Annotation Database Interface
AnnotationForge        Code for Building Annotation Database Packages
ape                    Analyses of Phylogenetics and Evolution
aplpack                Another Plot PACKage: stem.leaf, bagplot,
                        faces, spin3R, and some slider functions
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 on microarray data sets
aster                  Aster Models
auteur                  Bayesian sampler of the trait-evolutionary
                        process
aws                    Adaptive Weights Smoothing
awsMethods              Class and Methods definitions for packages aws,
                        adimpro, fmri, dwi
BAMD                    Bayesian Association Model for Genomic Data
                        with Missing Covariates
base                    The R Base Package
batchmeans              Consistent Batch Means Estimation of Monte
                        Carlo Standard Errors
BayesLogit              Logistic Regression
baySeq                  Empirical Bayesian analysis of patterns of
                        differential expression in count data
beadarray              Quality assessment and low-level analysis for
                        Illumina BeadArray data
BeadDataPackR          Compression of Illumina BeadArray data
Benchmarking            Benchmark and frontier analysis using DEA and
                        SFA
binom                  Binomial Confidence Intervals For Several
                        Parameterizations
Biobase                Biobase: Base functions for Bioconductor
BiocGenerics            Generic functions for Bioconductor
BiocInstaller          Install/Update Bioconductor and CRAN Packages
biomaRt                Interface to BioMart databases (e.g. Ensembl,
                        COSMIC ,Wormbase and Gramene)
biomod2                Ensemble platform for species distribution
                        modeling
Biostrings              String objects representing biological
                        sequences, and matching algorithms
biovizBase              Basic graphic utilities for visualization of
                        genomic data.
bit                    A class for vectors of 1-bit booleans
bitops                  Bitwise Operations
boot                    Bootstrap Functions (originally by Angelo Canty
                        for S)
BSgenome                Infrastructure for Biostrings-based genome data
                        packages
Cairo                  R graphics device using cairo graphics library
                        for creating high-quality bitmap (PNG, JPEG,
                        TIFF), vector (PDF, SVG, PostScript) and
                        display (X11 and Win32) output.
car                    Companion to Applied Regression
Category               Category Analysis
caTools                Tools: moving window statistics, GIF, Base64,
                        ROC AUC, etc.
ce25bmrv02cdf          ce25bmrv02cdf
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 distance-based clustering for
                        one-dimensional data
class                  Functions for Classification
cluster                Cluster Analysis Extended Rousseeuw et al.
CNVtools                A package to test genetic association with CNV
                        data
coda                    Output analysis and diagnostics for MCMC
codetools              Code Analysis Tools for R
colorspace              Color Space Manipulation
combinat                combinatorics utilities
compiler                The R Compiler Package
corpcor                Efficient Estimation of Covariance and
                        (Partial) Correlation
crlmm                  Genotype Calling (CRLMM) and Copy Number
                        Analysis tool for Affymetrix SNP 5.0 and 6.0
                        and Illumina arrays.
cummeRbund              Analysis, exploration, manipulation, and
                        visualization of Cufflinks high-throughput
                        sequencing data.
datasets                The R Datasets Package
DBI                    R Database Interface
deldir                  Delaunay Triangulation and Dirichlet (Voronoi)
                        Tessellation.
DESeq                  Differential gene expression analysis based on
                        the negative binomial distribution
deSolve                General Solvers for Initial Value Problems of
                        Ordinary Differential Equations (ODE), Partial
                        Differential Equations (PDE), Differential
                        Algebraic Equations (DAE), and Delay
                        Differential Equations (DDE)
DEXSeq                  Inference of differential exon usage in RNA-Seq
dichromat              Color Schemes for Dichromats
digest                  Create cryptographic hash digests of R objects
dismo                  Species distribution modeling
diversitree            diversitree: comparative phylogenetic analyses
                        of diversification
DNAcopy                DNA copy number data analysis
doMC                    Foreach parallel adaptor for the multicore
                        package
doParallel              Foreach parallel adaptor for the parallel
                        package
doSNOW                  Foreach parallel adaptor for the snow package
dynamicTreeCut          Methods for detection of clusters in
                        hierarchical clustering dendrograms.
DynDoc                  Dynamic document tools
e1071                  Misc Functions of the Department of Statistics
                        (e1071), TU Wien
edgeR                  Empirical analysis of digital gene expression
                        data in R
effects                Effect Displays for Linear, Generalized Linear,
                        Multinomial-Logit, Proportional-Odds Logit
                        Models and Mixed-Effects Models
ellipse                Functions for drawing ellipses and ellipse-like
                        confidence regions
FactoMineR              Multivariate Exploratory Data Analysis and Data
                        Mining with R
fastcluster            Fast hierarchical clustering routines for R and
                        Python
fda                    Functional Data Analysis
fdrtool                Estimation of (Local) False Discovery Rates and
                        Higher Criticism
FEAR                    Frontier Efficiency Analysis with R
ff                      memory-efficient storage of large data on disk
                        and fast access functions
flashClust              Implementation of optimal hierarchical
                        clustering
foreach                Foreach looping construct for R
foreign                Read Data Stored by Minitab, S, SAS, SPSS,
                        Stata, Systat, Weka, dBase, ...
Formula                Extended Model Formulas
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
gee                    Generalized Estimation Equation solver
geiger                  Analysis of evolutionary diversification
GeneCycle              Identification of Periodically Expressed Genes
genefilter              genefilter: methods for filtering genes from
                        microarray experiments
GeneNet                Modeling and Inferring Gene Networks
geneplotter            Graphics related functions for Bioconductor
GenomicFeatures        Tools for making and manipulating transcript
                        centric annotations
GenomicRanges          Representation and manipulation of genomic
                        intervals
geoR                    Analysis of geostatistical data
geoRglm                geoRglm - a package for generalised linear
                        spatial models
getopt                  C-like getopt behavior.
ggplot2                An implementation of the Grammar of Graphics
glmmADMB                Generalized Linear Mixed Models using AD Model
                        Builder
gmm                    Generalized Method of Moments and Generalized
                        Empirical Likelihood
gmodels                Various R programming tools for model fitting
GO.db                  A set of annotation maps describing the entire
                        Gene Ontology
GOstats                Tools for manipulating GO and microarrays.
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
graphics                The R Graphics Package
grDevices              The R Graphics Devices and Support for Colours
                        and Fonts
gregmisc                Greg's Miscellaneous Functions
grid                    The Grid Graphics Package
gridExtra              functions in Grid graphics
grofit                  The package was developed to fit fit many
                        growth curves obtained under different
                        conditions.
GSA                    Gene set analysis
gsalib                  Utility functions for GATK
GSEABase                Gene set enrichment data structures and methods
gsl                    wrapper for the Gnu Scientific Library
gstat                  spatial and spatio-temporal geostatistical
                        modelling, prediction and simulation
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
heatmap.plus            Heatmap with more sensible behavior.
hexbin                  Hexagonal Binning Routines
hglm                    Hierarchical Generalized Linear Models
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
HilbertVis              Hilbert curve visualization
Hmisc                  Harrell Miscellaneous
HSAUR2                  A Handbook of Statistical Analyses Using R (2nd
                        Edition)
hwriter                HTML Writer - Outputs R objects in HTML format
igraph                  Network analysis and visualization
igraph0                Network analysis and visualization, old,
                        deprecated package.
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 Approximaxion
inline                  Inline C, C++, Fortran function calls from R
intervals              Tools for working with points and intervals
IRanges                Infrastructure for manipulating intervals on
                        sequences
iterators              Iterator construct for R
itertools              Iterator Tools
KEGG.db                A set of annotation maps for KEGG
KEGGgraph              KEGGgraph: A graph approach to KEGG PATHWAY in
                        R and Bioconductor
KernSmooth              Functions for kernel smoothing for Wand & Jones
                        (1995)
ks                      Kernel smoothing
labeling                Axis Labeling
lars                    Least Angle Regression, Lasso and Forward
                        Stagewise
laser                  Likelihood Analysis of Speciation/Extinction
                        Rates from Phylogenies
lattice                Lattice Graphics
latticeExtra            Extra Graphical Utilities Based on Lattice
leaps                  regression subset selection
LearnBayes              Functions for Learning Bayesian Inference
limma                  Linear Models for Microarray Data
lme4                    Linear mixed-effects models using Eigen and S4
lmtest                  Testing Linear Regression Models
locfit                  Local Regression, Likelihood and Density
                        Estimation.
longitudinal            Analysis of Multiple Time Course Data
LPCM                    Local principal curve methods
lpridge                Local Polynomial (Ridge) Regression
lpSolveAPI              R Interface for lp_solve version 5.5.2.0
maanova                Tools for analyzing Micro Array experiments
magic                  create and investigate magic squares
mapproj                Map Projections
maps                    Draw Geographical Maps
maptools                Tools for reading and handling spatial objects
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
matrixcalc              Collection of functions for matrix calculations
matrixStats            Methods that apply to rows and columns of a
                        matrix
mclust                  Normal Mixture Modeling for Model-Based
                        Clustering, Classification, and Density
                        Estimation
MCMCpack                Markov chain Monte Carlo (MCMC) Package
mda                    Mixture and flexible discriminant analysis
memoise                Memoise functions
methods                Formal Methods and Classes
mgcv                    Mixed GAM Computation Vehicle with GCV/AIC/REML
                        smoothness estimation
minqa                  Derivative-free optimization algorithms by
                        quadratic approximation
misc3d                  Miscellaneous 3D Plots
msm                    Multi-state Markov and hidden Markov models in
                        continuous time
multcomp                Simultaneous Inference in General Parametric
                        Models
multicore              Parallel processing of R code on machines with
                        multiple cores or CPUs
multtest                Resampling-based multiple hypothesis testing
munsell                Munsell colour system
MVA                    An Introduction to Applied Multivariate
                        Analysis with R
mvtnorm                Multivariate Normal and t Distributions
ncbit                  retrieve and build NBCI taxonomic data
ncdf                    Interface to Unidata netCDF data files
ngspatial              Classes for Spatial Data
nlme                    Linear and Nonlinear Mixed Effects Models
nnet                    Feed-forward Neural Networks and Multinomial
                        Log-Linear Models
oligoClasses            Classes for high-throughput arrays supported by
                        oligo and crlmm
opm                    Tools for analysing OmniLog(R) Phenotype
                        Microarray data
org.Hs.eg.db            Genome wide annotation for Human
ouch                    Ornstein-Uhlenbeck models for phylogenetic
                        comparative hypotheses
parallel                Support for Parallel computation in R
pathview                a tool set for pathway based data integration
                        and visualization
permute                Functions for generating restricted
                        permutations of data
pheatmap                Pretty Heatmaps
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.
picante                R tools for integrating phylogenies and ecology
pixmap                  Bitmap Images (``Pixel Maps'')
pkgutils                pkgutils -- Utilities for creating R packages.
plier                  Implements the Affymetrix PLIER algorithm
plotrix                Various plotting functions
plyr                    Tools for splitting, applying and combining
                        data
png                    Read and write PNG images
preprocessCore          A collection of pre-processing functions
prettyR                Pretty descriptive stats.
pROC                    display and analyze ROC curves
proftools              Profile Output Processing Tools for R
proj4                  A simple interface to the PROJ.4 cartographic
                        projections library
proto                  Prototype object-based programming
PSCBS                  Analysis of Parent-Specific DNA Copy Numbers
pscl                    Political Science Computational Laboratory,
                        Stanford University
quantreg                Quantile Regression
qvalue                  Q-value estimation for false discovery rate
                        control
R2admb                  ADMB to R interface functions
R2jags                  A Package for Running jags from R
R2WinBUGS              Running WinBUGS and OpenBUGS from R / S-PLUS
RandomFields            Simulation and Analysis of Random Fields
randomForest            Breiman and Cutler's random forests for
                        classification and regression
RankProd                Rank Product method for identifying
                        differentially expressed genes with application
                        in meta-analysis
raster                  raster: Geographic data analysis and modeling
rasterVis              Visualization methods for the raster package
RBGL                    An interface to the BOOST graph library
R.cache                 Fast and light-weight caching (memoization) of
                        objects and results to speed up computations
Rcmdr                  R Commander
RColorBrewer            ColorBrewer palettes
Rcpp                    Seamless R and C++ Integration
RcppArmadillo          Rcpp integration for Armadillo templated linear
                        algebra library
RcppEigen              Rcpp integration for the Eigen templated linear
                        algebra library.
RCurl                  General network (HTTP/FTP/...) client interface
                        for R
R.devices              Unified handling of graphics devices
relimp                  Relative Contribution of Effects in a
                        Regression Model
reshape                Flexibly reshape data.
reshape2                Flexibly reshape data: a reboot of the reshape
                        package.
R.filesets              Easy handling of and access to files organized
                        in structured directories
rgdal                  Bindings for the Geospatial Data Abstraction
                        Library
rgeos                  Interface to Geometry Engine - Open Source
                        (GEOS)
rgl                    3D visualization device system (OpenGL)
Rgraphviz              Provides plotting capabilities for R graph
                        objects
R.huge                  Methods for accessing huge amounts of data
                        [DEPRECATED]
rjags                  Bayesian graphical models using MCMC
rjson                  JSON for R
RJSONIO                Serialize R objects to JSON, JavaScript Object
                        Notation
RMark                  R Code for MARK Analysis
R.methodsS3            Utility function for defining S3 methods
RMySQL                  R interface to the MySQL database
R.oo                    R object-oriented programming with or without
                        references
rpart                  Recursive Partitioning
R.rsp                  Dynamic generation of scientific reports
Rsamtools              Binary alignment (BAM), variant call (BCF), or
                        tabix file import
RSQLite                SQLite interface for R
RSQLite.extfuns        Math and String Extension Functions for RSQLite
Rsubread                Rsubread: an R package for the alignment,
                        summarization and analyses of next-generation
                        sequencing data
rtracklayer            R interface to genome browsers and their
                        annotation tracks
R.utils                Various programming utilities
Rwave                  Time-Frequency analysis of 1-D signals
sandwich                Robust Covariance Matrix Estimators
scales                  Scale functions for graphics.
scatterplot3d          3D Scatter Plot
sem                    Structural Equation Models
SemiPar                Semiparametic Regression
setRNG                  Set (Normal) Random Number Generator and Seed
siggenes                Multiple testing using SAM and Efron's
                        empirical Bayes approaches
simpleaffy              Very simple high level analysis of Affymetrix
                        data
snow                    Simple Network of Workstations
snowfall                Easier cluster computing (based on snow).
SNPchip                Visualizations for copy number alterations
sp                      classes and methods for spatial data
spacetime              classes and methods for spatio-temporal data
spam                    SPArse Matrix
SparseM                Sparse Linear Algebra
spatial                Functions for Kriging and Point Pattern
                        Analysis
spatstat                Spatial Point Pattern analysis, model-fitting,
                        simulation, tests
spBayes                Univariate and Multivariate Spatial-temporal
                        Modeling
spdep                  Spatial dependence: weighting schemes,
                        statistics and models
splancs                Spatial and Space-Time Point Pattern Analysis
splines                Regression Spline Functions and Classes
sqldf                  Perform SQL Selects on R Data Frames
statmod                Statistical Modeling
stats                  The R Stats Package
stats4                  Statistical Functions using S4 Classes
stringr                Make it easier to work with strings.
strucchange            Testing, Monitoring, and Dating Structural
                        Changes
subplex                Subplex optimization algorithm
survival                Survival Analysis
SVGAnnotation          Tools for post-processing SVG plots created in
                        R
tcltk                  Tcl/Tk Interface
tilingArray            Transcript mapping with high-density
                        oligonucleotide tiling arrays
tmvtnorm                Truncated Multivariate Normal and Student t
                        Distribution
tools                  Tools for Package Development
truncnorm              Truncated normal distribution
trust                  Trust Region Optimization
ucminf                  General-purpose unconstrained non-linear
                        optimization
unmarked                Models for Data from Unmarked Animals
utils                  The R Utils Package
vcd                    Visualizing Categorical Data
vegan                  Community Ecology Package
vsn                    Variance stabilization and calibration for
                        microarray data
waveslim                Basic wavelet routines for one-, two- and
                        three-dimensional signal processing
wavethresh              Wavelets statistics and transforms.
WGCNA                  Weighted Correlation Network Analysis
XML                    Tools for parsing and generating XML within R
                        and S-Plus.
xtable                  Export tables to LaTeX or HTML
xts                    eXtensible Time Series
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)
</pre>

Latest revision as of 13:59, 30 June 2017

File R_PACKAGES is missing.

Name Description