Difference between revisions of "R libraries"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
Moskalenko (talk | contribs) |
||
| Line 143: | Line 143: | ||
colorspace Color Space Manipulation | colorspace Color Space Manipulation | ||
compiler The R Compiler Package | compiler The R Compiler Package | ||
| + | corpcor Efficient Estimation of Covariance and | ||
| + | (Partial) Correlation | ||
crlmm Genotype Calling (CRLMM) and Copy Number | crlmm Genotype Calling (CRLMM) and Copy Number | ||
Analysis tool for Affymetrix SNP 5.0 and 6.0 | Analysis tool for Affymetrix SNP 5.0 and 6.0 | ||
| Line 191: | Line 193: | ||
Python | Python | ||
fda Functional Data Analysis | fda Functional Data Analysis | ||
| + | fdrtool Estimation of (Local) False Discovery Rates and | ||
| + | Higher Criticism | ||
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 206: | Line 210: | ||
genefilter genefilter: methods for filtering genes from | genefilter genefilter: methods for filtering genes from | ||
microarray experiments | microarray experiments | ||
| + | GeneNet Modeling and Inferring Gene Networks | ||
geneplotter Graphics related functions for Bioconductor | geneplotter Graphics related functions for Bioconductor | ||
GenomicFeatures Tools for making and manipulating transcript | GenomicFeatures Tools for making and manipulating transcript | ||
| Line 262: | Line 267: | ||
locfit Local Regression, Likelihood and Density | locfit Local Regression, Likelihood and Density | ||
Estimation. | Estimation. | ||
| + | longitudinal Analysis of Multiple Time Course Data | ||
lpridge Local Polynomial (Ridge) Regression | lpridge Local Polynomial (Ridge) Regression | ||
maanova Tools for analyzing Micro Array experiments | maanova Tools for analyzing Micro Array experiments | ||
Revision as of 21:17, 6 March 2013
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
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
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
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)
Biostrings String objects representing biological
sequences, and matching algorithms
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
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
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
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)
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.
CGHweb analyzing array_CGH data with multiple
algorithms
chron Chronological objects which can handle dates
and times
class Functions for Classification
cluster Cluster Analysis Extended Rousseeuw et al.
cnv Detection of Copy Number Variation by
Sequencing
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
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
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
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
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
EMA Easy Microarray data Analysis
exonmap High level analysis of Affymetrix exon array
data
exon.pmcdf exon.pmcdf
FactoMineR Multivariate Exploratory Data Analysis and Data
Mining with R
FASeg Forward-backward fragment assembling method for
the segmentation of array-based copy number
data
fastcluster Fast hierarchical clustering routines for R and
Python
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
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
GDD GD device for creating bitmap graphics as jpeg,
png or gif files using gd library
gee Generalized Estimation Equation solver
geiger Analysis of evolutionary diversification
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
ggplot2 An implementation of the Grammar of Graphics
GLAD Gain and Loss Analysis of DNA
glmmADMB Generalized Linear Mixed Models using AD Model
Builder
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
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
grid The Grid Graphics Package
GSA Gene set analysis
GSEABase Gene set enrichment data structures and methods
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.
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
latticeExtra Extra Graphical Utilities Based on Lattice
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.
longitudinal Analysis of Multiple Time Course Data
lpridge Local Polynomial (Ridge) Regression
maanova Tools for analyzing Micro Array experiments
maDB Microarray database and utility functions for
microarray data analysis.
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
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
oligoClasses Classes for high-throughput arrays supported by
oligo and crlmm
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
pgUtils Utility functions for PostgreSQL databases
pheatmap Pretty Heatmaps
phylobase Base package for phylogenetic structures and
comparative data
picante R tools for integrating phylogenies and ecology
pixmap Bitmap Images (``Pixel Maps'')
plier Implements the Affymetrix PLIER algorithm
plotrix Various plotting functions
plyr Tools for splitting, applying and combining
data
preprocessCore A collection of pre-processing functions
prettyR Pretty descriptive stats.
proto Prototype object-based programming
PSCBS Analysis of Parent-Specific DNA Copy Numbers
quantreg Quantile Regression
qvalue Q-value estimation for false discovery rate
control
R2admb ADMB to R interface functions
RankProd Rank Product method for identifying
differentially expressed genes with application
in meta-analysis
RBGL An interface to the BOOST graph library
R.cache Fast and light-weight caching (memoization) of
objects
Rcmdr R Commander
RColorBrewer ColorBrewer palettes
Rcpp Seamless R and C++ Integration
RcppEigen Rcpp integration for the Eigen templated linear
algebra library.
RCurl General network (HTTP/FTP/...) client interface
for R
R.devices Enhanced methods for handling graphical 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
rgl 3D visualization device system (OpenGL)
R.huge Methods for accessing huge amounts of data
[DEPRECATED]
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
RPostgreSQL R interface to the PostgreSQL database system
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: a super fast, sensitive and accurate
read aligner for mapping next-generation
sequencing reads
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
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
smida Statistics for Microarrays: Inference, Design
and Analysis
snapCGH Segmentation, normalisation and processing of
aCGH data.
snow Simple Network of Workstations
snowfall Easier cluster computing (based on snow).
SNPchip Visualizations for copy number alterations
SparseM Sparse Linear Algebra
spatial Functions for Kriging and Point Pattern
Analysis
splines Regression Spline Functions and Classes
spp some description
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, including penalised
sequencing reads
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
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
smida Statistics for Microarrays: Inference, Design
and Analysis
snapCGH Segmentation, normalisation and processing of
aCGH data.
snow Simple Network of Workstations
snowfall Easier cluster computing (based on snow).
SNPchip Visualizations for copy number alterations
SparseM Sparse Linear Algebra
spatial Functions for Kriging and Point Pattern
Analysis
splines Regression Spline Functions and Classes
spp some description
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, including penalised
likelihood.
SVGAnnotation Tools for post-processing SVG plots created in
R
tcltk Tcl/Tk Interface
tilingArray Transcript mapping with high-density
oligonucleotide tiling arrays
tools Tools for Package Development
truncnorm Truncated normal distribution
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)