Difference between revisions of "R libraries"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 231: | Line 231: | ||
Matrix Sparse and Dense Matrix Classes and Methods | Matrix Sparse and Dense Matrix Classes and Methods | ||
matrixcalc Collection of functions for matrix calculations | matrixcalc Collection of functions for matrix calculations | ||
| + | MatrixEQTL MatrixEQTL: Ultra fast eQTL analysis via large matrix operations | ||
matrixStats Methods that apply to rows and columns of a matrix | matrixStats Methods that apply to rows and columns of a matrix | ||
mboost Model-Based Boosting | mboost Model-Based Boosting | ||
Revision as of 20:07, 10 September 2014
a4Base Automated Affymetrix Array Analysis Base Package
a4Classif Automated Affymetrix Array Analysis Classification Package
a4Core Automated Affymetrix Array Analysis Core Package
a4Preproc Automated Affymetrix Array Analysis Preprocessing Package
a4Reporting Automated Affymetrix Array Analysis Reporting Package
abind Combine multi-dimensional arrays
aCGH Classes and functions for Array Comparative Genomic Hybridization data.
actuar Actuarial functions
ade4 Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences
afex Analysis of Factorial Experiments
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
AGDEX Agreement of Differential Expression Analysis
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, plotsummary, plothulls, 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
automap Automatic interpolation package
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
base64 Base 64 encoder/decoder
base64enc Tools for base64 encoding
batchmeans Consistent Batch Means Estimation of Monte Carlo Standard Errors
batman Bayesian AuTomated Metabolite Analyser for NMR spectra
BayesLogit Logistic Regression
baySeq Empirical Bayesian analysis of patterns of differential expression in count data
bdsmatrix Routines for Block Diagonal Symmetric matrices
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
biom An interface package (beta) for the BIOM file format.
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
BSgenome.Hsapiens.UCSC.hg19 Homo sapiens (Human) full genome (UCSC version hg19)
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.
CAMERA Collection of annotation related methods for mass spectrometry data
car Companion to Applied Regression
Category Category Analysis
caTools Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
CCA Canonical correlation analysis
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
coin Conditional Inference Procedures in a Permutation Test Framework
colorspace Color Space Manipulation
combinat combinatorics utilities
compiler The R Compiler Package
CompQuadForm Distribution function of quadratic forms in normal variables
corpcor Efficient Estimation of Covariance and (Partial) Correlation
coxme Mixed Effects Cox Models.
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
data.table Extension of data.frame
DBI R Database Interface
deldir Delaunay Triangulation and Dirichlet (Voronoi) Tessellation.
DESeq Differential gene expression analysis based on the negative binomial distribution
DESeq2 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
expm Matrix exponential
FactoMineR Multivariate Exploratory Data Analysis and Data Mining with R
fastcluster Fast hierarchical clustering routines for R and Python
fastmatch Fast match() function
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
ffbase Basic statistical functions for package ff
flashClust Implementation of optimal hierarchical clustering
fields Tools for spatial data
foreach Foreach looping construct for R
foreign Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka, dBase, ...
Formula Extended Model Formulas
gage Generally Applicable Gene-set Enrichment for Pathway Analysis
gageData Auxillary data for gage package
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.
ggmap A package for spatial visualization with Google Maps and OpenStreetMap
ggplot2 An implementation of the Grammar of Graphics
GLAD Gain and Loss Analysis of DNA
glmmADMB Generalized Linear Mixed Models using AD Model Builder
glmnet Lasso and elastic-net regularized generalized linear models
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)
httr Tools for working with URLs and HTTP
hwriter HTML Writer - Outputs R objects in HTML format
hydroGOF Goodness-of-fit functions for comparison of simulated and observed hydrological time
series
hydroTSM Time series management, analysis and interpolation for hydrological modelling
igraph Network analysis and visualization
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
jpeg Read and write JPEG images
KEGG.db A set of annotation maps for KEGG
KEGGgraph KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGREST Client-side REST access to KEGG
KernSmooth Functions for kernel smoothing for Wand & Jones (1995)
KFAS Kalman Filter and Smoother for Exponential Family State Space Models.
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
mapdata Extra Map Databases
mapproj Map Projections
maps Draw Geographical Maps
maptools Tools for reading and handling spatial objects
marray Exploratory analysis for two-color spotted microarray data
MARSS Multivariate Autoregressive State-Space Modeling
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
MatrixEQTL MatrixEQTL: Ultra fast eQTL analysis via large matrix operations
matrixStats Methods that apply to rows and columns of a matrix
mboost Model-Based Boosting
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
MLInterfaces Uniform interfaces to R machine learning procedures for data in Bioconductor containers
mmap Map Pages of Memory
modeltools Tools and Classes for Statistical Models
mombf Moment and Inverse Moment Bayes factors
monomvn Estimation for multivariate normal and Student-t data with monotone missingness
mpm Multivariate Projection Methods
msdata Various Mass Spectrometry raw data example files
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
mzR parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)
ncbit retrieve and build NBCI taxonomic data
ncdf Interface to Unidata netCDF data files
ncvreg Regularization paths for SCAD- and MCP-penalized regression models
ngspatial Classes for Spatial Data
nlme Linear and Nonlinear Mixed Effects Models
nnet Feed-forward Neural Networks and Multinomial Log-Linear Models
numDeriv Accurate Numerical Derivatives
oligo Preprocessing tools for oligonucleotide arrays.
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
pamr Pam: prediction analysis for microarrays
parallel Support for Parallel computation in R
pathview a tool set for pathway based data integration and visualization
pbkrtest Parametric bootstrap and Kenward Roger based methods for mixed model comparison
permute Functions for generating restricted permutations of data
pheatmap Pretty Heatmaps
phia Post-Hoc Interaction Analysis
phybase Basic functions for phylogenetic analysis
phyext An extension of some of the classes in phylobase. Tree objects now support subnodes on
branches
phybase Basic functions for phylogenetic analysis
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
pls Partial Least Squares and Principal Component regression
plyr Tools for splitting, applying and combining data
png Read and write PNG images
polyclip Polygon Clipping
pomp Statistical inference for partially observed Markov processes
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
ptw Parametric Time Warping
qqman Q-Q and manhattan plots for GWAS data
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
rda Shrunken Centroids Regularized Discriminant Analysis
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)
RgoogleMaps Overlays on Google map tiles in R
Rgraphviz Provides plotting capabilities for R graph objects
R.huge Methods for accessing huge amounts of data [DEPRECATED]
rjags Bayesian graphical models using MCMC
rJava Low-level R to Java interface
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
ROCR Visualizing the performance of scoring classifiers.
R.oo R object-oriented programming with or without references
rpanel Simple interactive controls for R using the tcltk library.
rpart Recursive Partitioning and Regression Trees
rrBLUP Ridge regression and other kernels for genomic selection
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: high-performance read alignment, quantification and mutation discovery
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
sealasso Standard Error Adjusted Adaptive Lasso
sem Structural Equation Models
SemiPar Semiparametic Regression
seqMeta An R package for meta-analyzing region-based tests of rare DNA variants
setRNG Set (Normal) Random Number Generator and Seed
sfsmisc Utilities from Seminar fuer Statistik ETH Zurich
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
spatial.tools R functions for working with spatial data.
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
tcltk2 Tcl/Tk Additions
tensor Tensor product of arrays
TH.data TH's Data Archive
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
TxDb.Hsapiens.UCSC.hg19.knownGene Annotation package for TranscriptDb object(s)
ucminf General-purpose unconstrained non-linear optimization
unmarked Models for Data from Unmarked Animals
utils The R Utils Package
varSelectIP Objective Bayes Model Selection
varSelRF Variable selection using random forests
vcd Visualizing Categorical Data
vegan Community Ecology Package
VGAM Vector Generalized Linear and Additive Models
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
xcms LC/MS and GC/MS Data Analysis
XML Tools for parsing and generating XML within R and S-Plus.
xps Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole
Genome Arrays and Plate Arrays
xtable Export tables to LaTeX or HTML
xts eXtensible Time Series
XVector Representation and manpulation of external sequences
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)