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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
| |
| 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
| |
| 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
| |
| 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)
| |
| Biostrings String objects representing biological
| |
| sequences, and matching algorithms
| |
| abind Combine multi-dimensional arrays
| |
| aCGH Classes and functions for Array Comparative
| |
| Genomic Hybridization data.
| |
| ade4 Analysis of Ecological Data : Exploratory and
| |
| Euclidean methods in Environmental sciences
| |
| 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
| |
| 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
| |
| 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
| |
| 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
| |
| 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)
| |
| 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.
| |
| CGHweb analyzing array_CGH data with multiple
| |
| algorithms
| |
| chron Chronological objects which can handle dates
| |
| and times
| |
| class Functions for Classification
| |
| cluster Cluster Analysis Extended Rousseeuw et al.
| |
| cnv Detection of Copy Number Variation by
| |
| Sequencing
| |
| 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
| |
| 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
| |
| 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
| |
| 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
| |
| EMA Easy Microarray data Analysis
| |
| exonmap High level analysis of Affymetrix exon array
| |
| data
| |
| exon.pmcdf exon.pmcdf
| |
| FactoMineR Multivariate Exploratory Data Analysis and Data
| |
| Mining with R
| |
| FASeg Forward-backward fragment assembling method for
| |
| the segmentation of array-based copy number
| |
| data
| |
| fastcluster Fast hierarchical clustering routines for R and
| |
| Python
| |
| fda Functional Data Analysis
| |
| fdrtool Estimation of (Local) False Discovery Rates and
| |
| Higher Criticism
| |
| 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, dBase, ...
| |
| gcrma Background Adjustment Using Sequence
| |
| Information
| |
| gdata Various R programming tools for data
| |
| manipulation
| |
| GDD GD device for creating bitmap graphics as jpeg,
| |
| png or gif files using gd library
| |
| 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
| |
| ggplot2 An implementation of the Grammar of Graphics
| |
| GLAD Gain and Loss Analysis of DNA
| |
| glmmADMB Generalized Linear Mixed Models using AD Model
| |
| Builder
| |
| 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
| |
| 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
| |
| GSA Gene set analysis
| |
| GSEABase Gene set enrichment data structures and methods
| |
| 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.
| |
| 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)
| |
| 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
| |
| impute impute: Imputation for microarray data
| |
| IRanges Infrastructure for manipulating intervals on
| |
| sequences
| |
| iterators Iterator construct for R
| |
| itertools Iterator Tools
| |
| KEGG.db A set of annotation maps for KEGG
| |
| KernSmooth Functions for kernel smoothing for Wand & Jones
| |
| (1995)
| |
| 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
| |
| limma Linear Models for Microarray Data
| |
| lme4 Linear mixed-effects models using S4 classes
| |
| lmtest Testing Linear Regression Models
| |
| locfit Local Regression, Likelihood and Density
| |
| Estimation.
| |
| longitudinal Analysis of Multiple Time Course Data
| |
| lpridge Local Polynomial (Ridge) Regression
| |
| maanova Tools for analyzing Micro Array experiments
| |
| maDB Microarray database and utility functions for
| |
| microarray data analysis.
| |
| 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
| |
| memoise Memoise functions
| |
| methods Formal Methods and Classes
| |
| mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML
| |
| smoothness estimation
| |
| 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
| |
| 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
| |
| org.Hs.eg.db Genome wide annotation for Human
| |
| ouch Ornstein-Uhlenbeck models for phylogenetic
| |
| comparative hypotheses
| |
| parallel Support for Parallel computation in R
| |
| permute Functions for generating restricted
| |
| permutations of data
| |
| pgUtils Utility functions for PostgreSQL databases
| |
| pheatmap Pretty Heatmaps
| |
| phylobase Base package for phylogenetic structures and
| |
| comparative data
| |
| picante R tools for integrating phylogenies and ecology
| |
| pixmap Bitmap Images (``Pixel Maps'')
| |
| plier Implements the Affymetrix PLIER algorithm
| |
| plotrix Various plotting functions
| |
| plyr Tools for splitting, applying and combining
| |
| data
| |
| preprocessCore A collection of pre-processing functions
| |
| prettyR Pretty descriptive stats.
| |
| proto Prototype object-based programming
| |
| PSCBS Analysis of Parent-Specific DNA Copy Numbers
| |
| quantreg Quantile Regression
| |
| qvalue Q-value estimation for false discovery rate
| |
| control
| |
| R2admb ADMB to R interface functions
| |
| RankProd Rank Product method for identifying
| |
| differentially expressed genes with application
| |
| in meta-analysis
| |
| RBGL An interface to the BOOST graph library
| |
| R.cache Fast and light-weight caching (memoization) of
| |
| objects
| |
| Rcmdr R Commander
| |
| RColorBrewer ColorBrewer palettes
| |
| Rcpp Seamless R and C++ Integration
| |
| RcppEigen Rcpp integration for the Eigen templated linear
| |
| algebra library.
| |
| RCurl General network (HTTP/FTP/...) client interface
| |
| for R
| |
| R.devices Enhanced methods for handling graphical 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
| |
| rgl 3D visualization device system (OpenGL)
| |
| Rgraphviz Provides plotting capabilities for R graph
| |
| objects
| |
| R.huge Methods for accessing huge amounts of data
| |
| [DEPRECATED]
| |
| 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
| |
| RPostgreSQL R interface to the PostgreSQL database system
| |
| 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: a super fast, sensitive and accurate
| |
| read aligner for mapping next-generation
| |
| sequencing reads
| |
| 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
| |
| 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
| |
| smida Statistics for Microarrays: Inference, Design
| |
| and Analysis
| |
| snapCGH Segmentation, normalisation and processing of
| |
| aCGH data.
| |
| snow Simple Network of Workstations
| |
| snowfall Easier cluster computing (based on snow).
| |
| SNPchip Visualizations for copy number alterations
| |
| SparseM Sparse Linear Algebra
| |
| spatial Functions for Kriging and Point Pattern
| |
| Analysis
| |
| splines Regression Spline Functions and Classes
| |
| spp some description
| |
| 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, including penalised
| |
| sequencing reads
| |
| 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
| |
| 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
| |
| smida Statistics for Microarrays: Inference, Design
| |
| and Analysis
| |
| snapCGH Segmentation, normalisation and processing of
| |
| aCGH data.
| |
| snow Simple Network of Workstations
| |
| snowfall Easier cluster computing (based on snow).
| |
| SNPchip Visualizations for copy number alterations
| |
| SparseM Sparse Linear Algebra
| |
| spatial Functions for Kriging and Point Pattern
| |
| Analysis
| |
| splines Regression Spline Functions and Classes
| |
| spp some description
| |
| 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, including penalised
| |
| likelihood.
| |
| SVGAnnotation Tools for post-processing SVG plots created in
| |
| R
| |
| tcltk Tcl/Tk Interface
| |
| tilingArray Transcript mapping with high-density
| |
| oligonucleotide tiling arrays
| |
| tools Tools for Package Development
| |
| truncnorm Truncated normal distribution
| |
| utils The R Utils Package
| |
| 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
| |
| zlibbioc An R packaged zlib-1.2.5
| |
| zoo S3 Infrastructure for Regular and Irregular
| |
| Time Series (Z's ordered observations)
| |
| </pre>
| |