Difference between revisions of "R libraries"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 33: | Line 33: | ||
basic R data types | basic R data types | ||
arrayQualityMetrics Quality metrics on microarray data sets | arrayQualityMetrics Quality metrics on microarray data sets | ||
| + | aster Aster Models | ||
auteur Bayesian sampler of the trait-evolutionary | auteur Bayesian sampler of the trait-evolutionary | ||
process | process | ||
| Line 38: | Line 39: | ||
awsMethods Class and Methods definitions for packages aws, | awsMethods Class and Methods definitions for packages aws, | ||
adimpro, fmri, dwi | adimpro, fmri, dwi | ||
| + | BAMD Bayesian Association Model for Genomic Data | ||
| + | with Missing Covariates | ||
base The R Base Package | 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 | baySeq Empirical Bayesian analysis of patterns of | ||
differential expression in count data | differential expression in count data | ||
| Line 139: | Line 145: | ||
fdrtool Estimation of (Local) False Discovery Rates and | fdrtool Estimation of (Local) False Discovery Rates and | ||
Higher Criticism | Higher Criticism | ||
| + | FEAR Frontier Efficiency Analysis with R | ||
ff memory-efficient storage of large data on disk | ff memory-efficient storage of large data on disk | ||
and fast access functions | and fast access functions | ||
| Line 145: | Line 152: | ||
foreach Foreach looping construct for R | foreach Foreach looping construct for R | ||
foreign Read Data Stored by Minitab, S, SAS, SPSS, | foreign Read Data Stored by Minitab, S, SAS, SPSS, | ||
| − | Stata, Systat, dBase, ... | + | Stata, Systat, Weka, dBase, ... |
Formula Extended Model Formulas | Formula Extended Model Formulas | ||
gam Generalized Additive Models | gam Generalized Additive Models | ||
| Line 207: | Line 214: | ||
heatmap.plus Heatmap with more sensible behavior. | heatmap.plus Heatmap with more sensible behavior. | ||
hexbin Hexagonal Binning Routines | hexbin Hexagonal Binning Routines | ||
| + | hglm Hierarchical Generalized Linear Models | ||
hgu133plus2.db Affymetrix Human Genome U133 Plus 2.0 Array | hgu133plus2.db Affymetrix Human Genome U133 Plus 2.0 Array | ||
annotation data (chip hgu133plus2) | annotation data (chip hgu133plus2) | ||
hgu95av2.db Affymetrix Human Genome U95 Set annotation data | hgu95av2.db Affymetrix Human Genome U95 Set annotation data | ||
(chip hgu95av2) | (chip hgu95av2) | ||
| + | hierNet A Lasso for Hierarchical Interactions | ||
HilbertVis Hilbert curve visualization | HilbertVis Hilbert curve visualization | ||
Hmisc Harrell Miscellaneous | Hmisc Harrell Miscellaneous | ||
| Line 221: | Line 230: | ||
illuminaio Parsing Illumina microarray output files | illuminaio Parsing Illumina microarray output files | ||
impute impute: Imputation for microarray data | 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 | intervals Tools for working with points and intervals | ||
IRanges Infrastructure for manipulating intervals on | IRanges Infrastructure for manipulating intervals on | ||
| Line 231: | Line 244: | ||
KernSmooth Functions for kernel smoothing for Wand & Jones | KernSmooth Functions for kernel smoothing for Wand & Jones | ||
(1995) | (1995) | ||
| + | ks Kernel smoothing | ||
labeling Axis Labeling | labeling Axis Labeling | ||
lars Least Angle Regression, Lasso and Forward | lars Least Angle Regression, Lasso and Forward | ||
| Line 241: | Line 255: | ||
LearnBayes Functions for Learning Bayesian Inference | LearnBayes Functions for Learning Bayesian Inference | ||
limma Linear Models for Microarray Data | limma Linear Models for Microarray Data | ||
| − | lme4 Linear mixed-effects models using S4 | + | lme4 Linear mixed-effects models using Eigen and S4 |
lmtest Testing Linear Regression Models | lmtest Testing Linear Regression Models | ||
locfit Local Regression, Likelihood and Density | locfit Local Regression, Likelihood and Density | ||
| Line 271: | Line 285: | ||
mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML | mgcv Mixed GAM Computation Vehicle with GCV/AIC/REML | ||
smoothness estimation | smoothness estimation | ||
| + | minqa Derivative-free optimization algorithms by | ||
| + | quadratic approximation | ||
| + | misc3d Miscellaneous 3D Plots | ||
msm Multi-state Markov and hidden Markov models in | msm Multi-state Markov and hidden Markov models in | ||
continuous time | continuous time | ||
| Line 283: | Line 300: | ||
mvtnorm Multivariate Normal and t Distributions | mvtnorm Multivariate Normal and t Distributions | ||
ncbit retrieve and build NBCI taxonomic data | 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 | nlme Linear and Nonlinear Mixed Effects Models | ||
nnet Feed-forward Neural Networks and Multinomial | nnet Feed-forward Neural Networks and Multinomial | ||
| Line 328: | Line 347: | ||
control | control | ||
R2admb ADMB to R interface functions | R2admb ADMB to R interface functions | ||
| + | R2jags A Package for Running jags from R | ||
R2WinBUGS Running WinBUGS and OpenBUGS from R / S-PLUS | R2WinBUGS Running WinBUGS and OpenBUGS from R / S-PLUS | ||
RandomFields Simulation and Analysis of Random Fields | RandomFields Simulation and Analysis of Random Fields | ||
| Line 366: | Line 386: | ||
R.huge Methods for accessing huge amounts of data | R.huge Methods for accessing huge amounts of data | ||
[DEPRECATED] | [DEPRECATED] | ||
| + | rjags Bayesian graphical models using MCMC | ||
rjson JSON for R | rjson JSON for R | ||
RJSONIO Serialize R objects to JSON, JavaScript Object | RJSONIO Serialize R objects to JSON, JavaScript Object | ||
| Line 432: | Line 453: | ||
tools Tools for Package Development | tools Tools for Package Development | ||
truncnorm Truncated normal distribution | truncnorm Truncated normal distribution | ||
| + | trust Trust Region Optimization | ||
ucminf General-purpose unconstrained non-linear | ucminf General-purpose unconstrained non-linear | ||
optimization | optimization | ||
Revision as of 16:25, 21 January 2014
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
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)