Difference between revisions of "R libraries"

Latest revision as of 13:59, 30 June 2017

File R_PACKAGES is missing.

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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
-affy                    Methods for Affymetrix Oligonucleotide Arrays
+|data=name=Package,description=Title
-affydata                Affymetrix Data for Demonstration Purpose
+|format=CSV with header
-affyio                  Tools for parsing Affymetrix data files
+|cache seconds=3600
-affyPLM                 Methods for fitting probe-level models
+}}
-affyQCReport            QC Report Generation for affyBatch objects
+{| class="wikitable"
-agricolae               Statistical Procedures for Agricultural
+! Name
-                        Research
+! Description {{#for_external_table:<nowiki/>
-akima                   Interpolation of irregularly spaced data
+{{!}}-
-annaffy                 Annotation tools for Affymetrix biological
+{{!}} {{{name}}}
-                        metadata
+{{!}} {{{description}}}}}
-annotate                Annotation for microarrays
+|}
-AnnotationDbi           Annotation Database Interface
-ape                     Analyses of Phylogenetics and Evolution
-aplpack                 Another Plot PACKage: stem.leaf, bagplot,
-                        faces, spin3R, and some slider functions
-auteur                  Bayesian sampler of the trait-evolutionary
-                        process
-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
-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
-bitops                  Functions for Bitwise operations
-boot                    Bootstrap Functions (originally by Angelo Canty
-                        for S)
-car                     Companion to Applied Regression
-caTools                 Tools: moving window statistics, GIF, Base64,
-                        ROC AUC, etc.
-chron                   Chronological objects which can handle dates
-                        and times
-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
-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
-DEXSeq                  Inference of differential exon usage in RNA-Seq
-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
-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
-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
-gsubfn                  Utilities for strings and function arguments.
-gtools                  Various R programming tools
-hacks                   Convenient R Functions
-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
-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
-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.
-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
-matrixcalc              Collection of functions for matrix differential
-                        calculus
-mclust                  Normal Mixture Modeling for Model-Based
-                        Clustering, Classification, and Density
-                        Estimation
-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
-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]
-Rcmdr                   R Commander
-RColorBrewer            ColorBrewer palettes
-Rcpp                    Seamless R and C++ Integration
-RCurl                   General network (HTTP/FTP/...) client interface
-                        for R
-relimp                  Relative Contribution of Effects in a
-                        Regression Model
-reshape                 Flexibly reshape data.
-reshape2                Flexibly reshape data: a reboot of the reshape
-                        package.
-rgl                     3D visualization device system (OpenGL)
-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
-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
-R.utils                 Various programming utilities
-Rwave                   Time-Frequency analysis of 1-D signals
-scales                  Scale functions for graphics.
-scatterplot3d           3D Scatter Plot
-sem                     Structural Equation Models
-simpleaffy              Very simple high level analysis of Affymetrix
-                        data
-smida                   Statistics for Microarrays: Inference, Design
-                        and Analysis
-snow                    Simple Network of Workstations
-spatial                 Functions for Kriging and 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.
-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>