Difference between revisions of "R libraries"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) |
|||
| Line 320: | Line 320: | ||
oligonucleotide tiling arrays | oligonucleotide tiling arrays | ||
tools Tools for Package Development | tools Tools for Package Development | ||
| + | truncnorm Truncated normal distribution | ||
utils The R Utils Package | utils The R Utils Package | ||
vegan Community Ecology Package | vegan Community Ecology Package | ||
Revision as of 03:27, 15 January 2013
abind Combine multi-dimensional arrays
aCGH Classes and functions for Array Comparative
Genomic Hybridization data.
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
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
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
bit A class for vectors of 1-bit booleans
bitops 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.
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.
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
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
DEXSeq Inference of differential exon usage in RNA-Seq
dichromat Color schemes for dichromats
digest Create cryptographic hash digests of R objects
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
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
fda Functional Data Analysis
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
geneplotter Graphics related functions for Bioconductor
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
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.
gtable Arrange grobs in tables.
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 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
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
quantreg Quantile Regression
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]
R.cache Fast and light-weight caching (memoization) of
objects
Rcmdr R Commander
RColorBrewer ColorBrewer palettes
Rcpp Seamless R and C++ Integration
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
R.rsp Dynamic generation of scientific reports
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
sandwich Robust Covariance Matrix Estimators
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
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
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.
tcltk Tcl/Tk Interface
tilingArray Transcript mapping with high-density
oligonucleotide tiling arrays
tools Tools for Package Development
utils The R Utils Package
vegan Community Ecology Package
sequencing reads
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
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
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.
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)