My Microarray Software Comparison - R packages for microarray analysis

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Definition of R packages for microarray analysis
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General R packages useful for microarray analysis (in alphabetical order)

R packages for microarray analysis (in alphabetical order)

Definition of R packages for microarray analysis

Any R packages that are specifically written or useful for microarray data analysis; R environment is required for running these packages. Some S-plus programs will also be listed here.

General R packages useful for microarray analysis (in alphabetical order)

Package	Author	Features	Licence	Remarks
amap (Another Multidimensional Analysis Package)	Antoine Lucas	amap is a package for Hierarchical clustering (optimised for memory), generalised PCA and graphics for PCA.	?	download from author's site (unix/linux);manual; link at CRAN
cclust (Convex Clustering Methods and Clustering Indexes)	Evgenia Dimitriadou	Convex Clustering methods, including Kmeans algorithm, On-line Update algorithm (Hard Competitive Learning) and Neural Gas algorithm (Soft Competitive Learning) and calculation of several indexes for finding the number of clusters in a data set.	GNU GPL (version 2 or later)	download (unix/ linux) (windows);index;manual
CGH-Miner	Stanford University	Identifies DNA copy number alterations for CGH arrays using the "Cluster Along Chromosomes (CLAC)" method	?	download (windows); manual; Reference [pdf]
cluster	S original by Peter Rousseeuw, Anja Struyf , Mia Hubert. R port by Kurt Hornik and Martin Maechler.	Functions for cluster analysis	GNU GPL (version 2 or later)	download (unix/ linux) (windows);index;manual
e1071	Evgenia Dimitriadou, Kurt Hornik, Friedrich Leisch, David Meyer, and Andreas Weingessel	Functions for latent class analysis, short time Fourier transform, fuzzy clustering, support vector machines, shortest path computation, bagged clustering, ...	GPL version 2.	download (unix/ linux) (windows);index;manual
mclust	C. Fraley and A.E. Raftery. R port by Ron Wehrens	Model-based cluster analysis	Permission granted for unlimited redistribution for non-commercial use only	download (unix/ linux) (windows);index;manual; website;
multiv (Multivariate Data Analysis Routines)	S original by F. Murtagh . R port by Kurt Hornik, Friedrich Leisch and Achim Zeileis	Multivariate Data Analysis Routines including hierarchical clustering, PCA, Sammon mapping, correspondence analysis	Free re-distribution for non-commercial purposes.	download (unix/ linux) (windows);index;manual;
mva	-	Classical Multivariate Analysis, contains functions for hierarchical and k-means clustering, PCA, dendrogram and heatmap drawing	GNU GPL (version 2 or later)	a basic component of R

R packages for microarray analysis (in alphabetical order)

Package	Author	Feature	Licence	Remarks
ANOVA model for time course experiment	Park T et al.,	A statistical test procedure based on the ANOVA model to identify genes that have different gene expression profiles among experimental groups in time-course experiments.	-	Reference [PubMed]; available upon request
affy (Methods for Affymetrix Oligonucleotide Arrays)	Rafael A. Irizarry, Laurent Gautier, Biostatistics Department; Johns Hopkins University.	The package contains some methods for analyses of affymetrix oligonucleotide array data.	GNU GPL (version 2 or later)	description [pdf]; affy is now a part of the BioConductor project
BioConductor	many	an open source software project with several goals. Main goals: providing infrastructure in terms of design and software for analysing genomic data, some form of graphical user interface for selected libraries and a mechanism for linking together different groups with common goal	GNU GPL (version 2 or later)	current released packages; current developmental packages; contributed packages; faq;Vignettes; Short Courses (very useful!); Research Talks; An excellent introductory tutorial by Chis Bye; GUI for package Limma;
BUM	Pounds S, Morris SW. Department of Biostatistics, St. Jude Children's Research Hospital	Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values.	?	download (S-plus); user guide; reference [PubMed]
CTC (Cluster and Tree Conversion)	Antoine Lucas	exports R tables to Xcluster and Cluster; imports Xcluster and Cluster output to R	?	download (unix/linux), (windows);manual;
CyberT	Tony Long and Harry Mangalam (UC Irvine)	t-test for statistically significant differences between sample sets for arrays; Bayesian probabilistic framework to estimate the variance among replicates	GNU GPL (version 2 or later)	download;help
Emerging Patterns	Boulesteix AL, Tutz G, Strimmer K.	A CART-based approach to discover EPs in microarray data. The method is based on growing decision trees from which the EPs are extracted. This approach combines pattern search with a statistical procedure based on Fisher's exact test to assess the significance of each EP. Subsequently, sample classification based on the inferred EPs is performed using maximum-likelihood linear discriminant analysis.	GNU GPL	R codes; Readme; examples; reference [PubMed]
EMV	Raphael Gottardo	Estimation of missing values in a matrix by a k-th nearest neighboors algorithm	GPL version 2 or later	download (unix/linux), (windows); manual; reference[PubMed][pdf]
FDR controlling procedures	Anat Reiner, Daniel Yekutieli and Yoav Benjamini	adjusts p-values generated in multiple hypothesis testing of gene expression data obtained by cDNA microarray experiment.	-	download (R); (S-plus) ; reference [PubMed][doc]
FEXAT	Kraft P, Schadt EE, Aten J, Horvath S	A family-based test for correlation between gene expression and trait values	free	download; reference [PubMed]
GeneClust	Kim-Anh Do	GeneClust is a piece of computer software which can be used as a tool for exploratory analysis of gene expression microarray data; hierarchical and gene shaving; Simulation to assess the clustering performance	?	Require Unix/Linux or Windows 2000 running S-plus!
GeneSOM	Jun Yan	Clustering Genes using Self-Organizing Map	GNU GPL (version 2 or later)	download (unix/ linux) (windows);index;manual;
GeneTS	Wichert S, Fokianos K, Strimmer K	some functions useful for microarray time series analysis, in particular cell cycle analysis and inferring graphical models from microarray data.	GNU GPL	download (unix/linux) (windows); reference [PubMed]
GIN (Gene Index)	LeBlanc M et al.,	a gene index technique that generalizes methods that rank genes by their univariate associations to patient outcome. Genes are ordered based on simultaneously linking their expression both to patient outcome and to a specific gene of interest.	-	download; Reference [PubMed];
HighProbability	David R. Bickel	HighProbability estimates which genes have frequentist or Bayesian probabilities of differential expression at least as great as a specified threshold, given a list of p-values.	Mozilla Public License 1.1 (http://www.mozilla.org/MPL/)	source; windows binary; manual;
Impute	Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu	Imputation for microarray data (currently KNN only)	GPL2.0	download (unix/linux) (windows); index; manual;
LogitBoost	Dettling, Marcel and Bühlmann, Peter	a feature preselection method, a more robust boosting procedure and a new approach for multi-categorical problems for supervised classification	Free	download (unix/linux) (windows); manual [ps][pdf] Reference [PubMed][pdf][ps]
mixture modelling	Debashis Ghosh	Mixture modelling of gene expression data from microarray experiments	?	download; paper (pdf), (ps); require mva and mclust.
MLE adjustment for signal censoring	Ernst Wit	The function calculates the maximum likelihood estimate of the parameters for a Gamma(alpha, beta) pixel intensity model, when only the mean, median variance and number of pixels are given.	Free?	Reference [PubMed]
PAM (Prediction Analysis for Microarrays)	Tibshirani Lab, Department of Statistics, Stanford University	Performs sample classification from gene expression data, Estimates prediction error via cross-validation, Provides a list of significant genes whose expression characterizes each diagnostic class	GPL2.0	download (unix/linux) (windows);manual; paper (pdf); documentation on nearest shrunken centroid classification; sample plots; reference[pdf]
permax	Robert J. Gray	The permax library consists of 7 functions, intended to facilitate certain basic analyses of DNA array data, especially with regard to comparing expression levels between two types of tissue.	GNU GPL 2	download (unix/linux) (windows);index;manual;
phyloarray	Kurt Sys	Software to process data from phylogenetic or identification microarrays. At present state, it is rather limited and focuss was on a fast and easy way for calculating background values by interpolation and plotting melting curves. The functions for reading the data are similar to those used in package 'sma' (statistical microarray analysis).	GNU GPL 2	download (unix/linux) (windows); index; manual;
POE (Probability of Expression)	Elizabeth Garrett, Jiang Hu, Giovanni Parmigiani, Rob Scharpf	statistical approaches to molecular classification that emphasize simple molecular profiles based on latent categories signifying under-, over-, and baseline-expression.	GNU GPL 2	download (linux); Reference [PubMed][pdf]
OOMAL (Object-Oriented Microarray Analysis Library) (* require S-PLUS!)	MD Anderson Cancer Center, The University of Texas	Object-oriented library for analyzing microarray data in S-PLUS, flexible tools for loading raw quantification data from a variety of microarray formats, normalization, identified differentially expressed genes, classification and discrimination between samples.	?	download source code; documentation;
qvalue	John D. Storey	for calculating q-values in multiple testing situations	?	download source code (please send the author an email with "qvalue download" in the subject line); manual;
R/maanova	Gary Churchill's Statistical Genetics Group, The Jackson Laboratory	R/maanova is an extensible, interactive environment for the analysis of variance on microarray data.	free for academic	registration before download; reference 1[pdf]; reference 2[pdf]
SMA (Statisics for Microarray Analysis)	Sandrine Dudoit,Yee Hwa (Jean) Yang, Benjamin Milo BOLSTAD (UC Berkeley)	The package contains some simple functions for exploratory microarray analysis, M-A plots, lowess curve fitting, handles replicate array data by Bayesian methods	GNU GPL (version 2 or later)	download (unix/ linux) (windows);help;index;manual; paper 1,2,3.
SMA extension (com.braju.sma)	Henrik Bengtsson	extensions of SMA	?	download (unix/ linux) (windows); documentation;presentation; requires SMA library and R.classesinstalled
Spot	CSIRO Mathematical and Information Sciences	Spot is a software package for the analysis of microarray images; Automatic grid location; Flexible spot segmentation; Morphological background estimation.	Commerical package; price depends on number of users	User guide; installation instruction; Demo version available upon registration
Statomics	David Bickel	Statomics is a software suite for the statistical analysis of genomic and proteomic data.	?	source code; Reference [PubMed][pdf]
VSN	Wolfgang Huber; Molecular Genome Analysis National Cancer Research Institute of Germany	Variance stabilization applied to microarray data calibration and to the quantification of differential expression	Free for academic use	Reference [PubMed][pdf]
YASMA (Yet Another Statistical Microarray Analysis)	Lorenz Wernisch and others	correlation between array replicates, ANOVA analysis, p- values for ANOVA analysis, standard t-tests	?	download(unix/linux);tutorial;related statistical notes; reference [PubMed][pdf]

last updated: 16 Jul 2004
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