Difference between revisions of "R libraries"

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Difference between revisions of "R libraries"

Latest revision as of 13:59, 30 June 2017

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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>