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| <pre>
| | [[Category:Software]] |
| affy Methods for Affymetrix Oligonucleotide Arrays
| | {{#get_file_data:file=R_PACKAGES |
| affydata Affymetrix Data for Demonstration Purpose
| | |data=name=Package,description=Title |
| affyio Tools for parsing Affymetrix data files
| | |format=CSV with header |
| affyPLM Methods for fitting probe-level models
| | |cache seconds=3600 |
| affyQCReport QC Report Generation for affyBatch objects
| | }} |
| akima Interpolation of irregularly spaced data
| | {| class="wikitable" |
| annaffy Annotation tools for Affymetrix biological
| | ! Name |
| metadata
| | ! Description {{#for_external_table:<nowiki/> |
| annotate Annotation for microarrays
| | {{!}}- |
| AnnotationDbi Annotation Database Interface
| | {{!}} {{{name}}} |
| ape Analyses of Phylogenetics and Evolution
| | {{!}} {{{description}}}}} |
| auteur Bayesian sampler of the trait-evolutionary
| | |} |
| process
| |
| base The R Base Package
| |
| baySeq Empirical Bayesian analysis of patterns of
| |
| differential expression in count data
| |
| Biobase Biobase: Base functions for Bioconductor
| |
| BiocGenerics Generic functions for Bioconductor
| |
| BiocInstaller Install/Update Bioconductor and CRAN Packages
| |
| Biostrings String objects representing biological
| |
| sequences, and matching algorithms
| |
| bitops Functions for Bitwise operations
| |
| boot Bootstrap Functions (originally by Angelo Canty
| |
| for S)
| |
| caTools Tools: moving window statistics, GIF, Base64,
| |
| ROC AUC, etc.
| |
| class Functions for Classification
| |
| cluster Cluster Analysis Extended Rousseeuw et al.
| |
| CNVtools A package to test genetic association with CNV
| |
| data
| |
| codetools Code Analysis Tools for R
| |
| colorspace Color Space Manipulation
| |
| compiler The R Compiler Package
| |
| 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
| |
| dichromat Color schemes for dichromats
| |
| digest Create cryptographic hash digests of R objects
| |
| doMC Foreach parallel adaptor for the multicore
| |
| package
| |
| doParallel Foreach parallel adaptor for the parallel
| |
| package
| |
| doSNOW Foreach parallel adaptor for the snow package
| |
| DynDoc Dynamic document tools
| |
| edgeR Empirical analysis of digital gene expression
| |
| data in R
| |
| ellipse Functions for drawing ellipses and ellipse-like
| |
| confidence regions
| |
| exon.pmcdf exon.pmcdf
| |
| FactoMineR Multivariate Exploratory Data Analysis and Data
| |
| | |
| 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
| |
| akima Interpolation of irregularly spaced data
| |
| annaffy Annotation tools for Affymetrix biological
| |
| metadata
| |
| annotate Annotation for microarrays
| |
| AnnotationDbi Annotation Database Interface
| |
| ape Analyses of Phylogenetics and Evolution
| |
| auteur Bayesian sampler of the trait-evolutionary
| |
| process
| |
| base The R Base Package
| |
| baySeq Empirical Bayesian analysis of patterns of
| |
| differential expression in count data
| |
| Biobase Biobase: Base functions for Bioconductor
| |
| BiocGenerics Generic functions for Bioconductor
| |
| BiocInstaller Install/Update Bioconductor and CRAN Packages
| |
| Biostrings String objects representing biological
| |
| sequences, and matching algorithms
| |
| bitops Functions for Bitwise operations
| |
| boot Bootstrap Functions (originally by Angelo Canty
| |
| for S)
| |
| caTools Tools: moving window statistics, GIF, Base64,
| |
| ROC AUC, etc.
| |
| class Functions for Classification | |
| cluster Cluster Analysis Extended Rousseeuw et al.
| |
| CNVtools A package to test genetic association with CNV
| |
| data
| |
| codetools Code Analysis Tools for R
| |
| colorspace Color Space Manipulation
| |
| compiler The R Compiler Package
| |
| 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
| |
| dichromat Color schemes for dichromats
| |
| digest Create cryptographic hash digests of R objects
| |
| doMC Foreach parallel adaptor for the multicore
| |
| package
| |
| doParallel Foreach parallel adaptor for the parallel
| |
| package
| |
| doSNOW Foreach parallel adaptor for the snow package
| |
| DynDoc Dynamic document tools
| |
| edgeR Empirical analysis of digital gene expression
| |
| data in R
| |
| ellipse Functions for drawing ellipses and ellipse-like
| |
| confidence regions
| |
| exon.pmcdf exon.pmcdf
| |
| FactoMineR Multivariate Exploratory Data Analysis and Data
| |
| Mining with R
| |
| fda Functional Data Analysis
| |
| 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
| |
| gee Generalized Estimation Equation solver
| |
| geiger Analysis of evolutionary diversification
| |
| genefilter genefilter: methods for filtering genes from
| |
| microarray experiments
| |
| geneplotter Graphics related functions for Bioconductor
| |
| GenomicRanges Representation and manipulation of genomic
| |
| intervals
| |
| ggplot2 An implementation of the Grammar of Graphics
| |
| glmmADMB Generalized Linear Mixed Models using AD Model
| |
| Builder
| |
| GO.db A set of annotation maps describing the entire
| |
| Gene Ontology
| |
| gplots Various R programming tools for plotting data
| |
| graphics The R Graphics Package
| |
| grDevices The R Graphics Devices and Support for Colours
| |
| and Fonts
| |
| grid The Grid Graphics Package
| |
| gtools Various R programming tools
| |
| hacks Convenient R Functions
| |
| hgu95av2.db Affymetrix Human Genome U95 Set annotation data
| |
| (chip hgu95av2)
| |
| HilbertVis Hilbert curve visualization
| |
| Hmisc Harrell Miscellaneous
| |
| 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
| |
| laser Likelihood Analysis of Speciation/Extinction
| |
| Rates from Phylogenies
| |
| lattice Lattice Graphics
| |
| leaps regression subset selection
| |
| limma Linear Models for Microarray Data
| |
| locfit Local Regression, Likelihood and Density
| |
| Estimation.
| |
| lpridge Local Polynomial (Ridge) Regression
| |
| maanova Tools for analyzing Micro Array experiments
| |
| 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
| |
| 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
| |
| multicore Parallel processing of R code on machines with
| |
| multiple cores or CPUs
| |
| multtest Resampling-based multiple hypothesis testing
| |
| munsell Munsell colour system
| |
| mvtnorm Multivariate Normal and t Distributions
| |
| nlme Linear and Nonlinear Mixed Effects Models
| |
| nnet Feed-forward Neural Networks and Multinomial
| |
| Log-Linear Models
| |
| 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
| |
| pheatmap Pretty Heatmaps
| |
| phylobase Base package for phylogenetic structures and
| |
| comparative data
| |
| picante R tools for integrating phylogenies and ecology
| |
| plyr Tools for splitting, applying and combining
| |
| data
| |
| preprocessCore A collection of pre-processing functions
| |
| prettyR Pretty descriptive stats.
| |
| proto Prototype object-based programming
| |
| qvalue Q-value estimation for false discovery rate
| |
| control
| |
| R2admb ADMB to R interface functions
| |
| R.basic [R] Class Library - Stand-alone basic functions
| |
| [DEPRECATED]
| |
| RColorBrewer ColorBrewer palettes
| |
| Rcpp Seamless R and C++ Integration
| |
| reshape Flexibly reshape data.
| |
| reshape2 Flexibly reshape data: a reboot of the reshape
| |
| package.
| |
| R.methodsS3 Utility function for defining S3 methods
| |
| R.oo R object-oriented programming with or without
| |
| references
| |
| rpart Recursive Partitioning
| |
| RSQLite SQLite interface for R
| |
| Rsubread Rsubread: a super fast, sensitive and accurate
| |
| read aligner for mapping next-generation
| |
| sequencing reads
| |
| R.utils Various programming utilities
| |
| Rwave Time-Frequency analysis of 1-D signals
| |
| scales Scale functions for graphics.
| |
| scatterplot3d 3D Scatter Plot
| |
| simpleaffy Very simple high level analysis of Affymetrix
| |
| data
| |
| snow Simple Network of Workstations
| |
| spatial Functions for Kriging and Point Pattern
| |
| Analysis
| |
| splines Regression Spline Functions and Classes
| |
| statmod Statistical Modeling
| |
| | |
| stats The R Stats Package
| |
| stats4 Statistical Functions using S4 Classes
| |
| stringr Make it easier to work with strings.
| |
| subplex Subplex optimization algorithm
| |
| survival Survival analysis, including penalised
| |
| likelihood.
| |
| tcltk Tcl/Tk Interface
| |
| tools Tools for Package Development
| |
| 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.
| |
| 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>
| |