eisa: Expression data analysis via the Iterative Signature Algorithm

The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("eisa")
AuthorGabor Csardi <csardi.gabor@gmail.com>
Bioconductor views Classification GeneExpression Microarray Visualization
Date of publicationNone
MaintainerGabor Csardi <csardi.gabor@gmail.com>
LicenseGPL (>= 2)
Version1.28.0

View on Bioconductor

Functions

ALLModules Man page
ALLModulesSmall Man page
annotate Man page
annotation,ISAModules-method Man page
anrichment Man page
CHRListHyperGParams Man page
CHRListHyperGParams-class Man page
CHRListHyperGResult Man page
CHRListHyperGResult-class Man page
class:ISAModules Man page
coerce,Biclust,ISAModules-method Man page
coerce,ISAModules,Biclust-method Man page
condGeneIdUniverse,CHRListHyperGResult-method Man page
condGeneIdUniverse,GeneralListHyperGResult-method Man page
condGeneIdUniverse,GOListHyperGResult-method Man page
condGeneIdUniverse,KEGGListHyperGResult-method Man page
condGeneIdUniverse,ListHyperGResult-method Man page
condGeneIdUniverse,miRNAListHyperGResult-method Man page
conditional<-,GOListHyperGParams,logical-method Man page
conditional,GOListHyperGParams-method Man page
conditional,GOListHyperGResult-method Man page
condPlot Man page
dim,ISAModules-method Man page
drive Man page
drive<- Man page
drive<-,CHRListHyperGParams,logical-method Man page
drive,CHRListHyperGParams-method Man page
drive<-,GeneralListHyperGParams,logical-method Man page
drive,GeneralListHyperGParams-method Man page
drive<-,GOListHyperGParams,logical-method Man page
drive,GOListHyperGParams-method Man page
drive<-,KEGGListHyperGParams,logical-method Man page
drive,KEGGListHyperGParams-method Man page
drive<-,ListHyperGParams,logical-method Man page
drive,ListHyperGParams-method Man page
drive<-,miRNAListHyperGParams,logical-method Man page
drive,miRNAListHyperGParams-method Man page
expectedCounts,CHRListHyperGResult-method Man page
expectedCounts,GeneralListHyperGResult-method Man page
expectedCounts,GOListHyperGResult-method Man page
expectedCounts,KEGGListHyperGResult-method Man page
expectedCounts,ListHyperGResult-method Man page
expectedCounts,miRNAListHyperGResult-method Man page
expPlot Man page
expPlotColbar Man page
expPlotCreate Man page
featExprs Man page
featExprs,ISAExpressionSet-method Man page
featureNames,ISAModules-method Man page
featureThreshold Man page
featureThreshold,ISAModules-method Man page
geneCounts,CHRListHyperGResult-method Man page
geneCounts,GeneralListHyperGResult-method Man page
geneCounts,GOListHyperGResult-method Man page
geneCounts,KEGGListHyperGResult-method Man page
geneCounts,ListHyperGResult-method Man page
geneCounts,miRNAListHyperGResult-method Man page
geneIdsByCategory,CHRListHyperGResult-method Man page
geneIdsByCategory,GeneralListHyperGResult-method Man page
geneIdsByCategory,GOListHyperGResult-method Man page
geneIdsByCategory,KEGGListHyperGResult-method Man page
geneIdsByCategory,ListHyperGResult-method Man page
geneIdsByCategory,miRNAListHyperGResult-method Man page
geneIdUniverse,CHRListHyperGResult-method Man page
geneIdUniverse,GeneralListHyperGResult-method Man page
geneIdUniverse,GOListHyperGResult-method Man page
geneIdUniverse,KEGGListHyperGResult-method Man page
geneIdUniverse,ListHyperGResult-method Man page
geneIdUniverse,miRNAListHyperGResult-method Man page
geneMappedCount,CHRListHyperGResult-method Man page
geneMappedCount,GeneralListHyperGResult-method Man page
geneMappedCount,GOListHyperGResult-method Man page
geneMappedCount,KEGGListHyperGResult-method Man page
geneMappedCount,ListHyperGResult-method Man page
geneMappedCount,miRNAListHyperGResult-method Man page
GeneralListHyperGParams Man page
GeneralListHyperGParams-class Man page
GeneralListHyperGResult Man page
GeneralListHyperGResult-class Man page
getFeatureMatrix Man page
getFeatureMatrix,ISAModules-method Man page
getFeatureNames Man page
getFeatureNames,ISAModules-method Man page
getFeatures Man page
getFeatureScores Man page
getFeatureScores,ISAModules-method Man page
getFeatures,ISAModules-method Man page
getFullFeatureMatrix Man page
getFullFeatureMatrix,ISAModules-method Man page
getFullSampleMatrix Man page
getFullSampleMatrix,ISAModules-method Man page
getNoFeatures Man page
getNoFeatures,ISAModules-method Man page
getNoSamples Man page
getNoSamples,ISAModules-method Man page
getOrganism Man page
getOrganism,ISAModules-method Man page
getSampleMatrix Man page
getSampleMatrix,ISAModules-method Man page
getSampleNames Man page
getSampleNames,ISAModules-method Man page
getSamples Man page
getSampleScores Man page
getSampleScores,ISAModules-method Man page
getSamples,ISAModules-method Man page
gograph Man page
gographPlot Man page
GOListHyperGParams Man page
GOListHyperGParams-class Man page
GOListHyperGResult Man page
GOListHyperGResult-class Man page
hasNA Man page
hasNA<- Man page
hasNA<-,ISAExpressionSet-method Man page
hasNA,ISAExpressionSet-method Man page
htmlReport,CHRListHyperGResult-method Man page
htmlReport,GeneralListHyperGResult-method Man page
htmlReport,GOListHyperGResult-method Man page
htmlReport,KEGGListHyperGResult-method Man page
htmlReport,ListHyperGResult-method Man page
htmlReport,miRNAListHyperGResult-method Man page
hyperGTest,CHRListHyperGParams-method Man page
hyperGTest,GeneralListHyperGParams-method Man page
hyperGTest,GOListHyperGParams-method Man page
hyperGTest,KEGGListHyperGParams-method Man page
hyperGTest,ListHyperGParams-method Man page
hyperGTest,miRNAListHyperGParams-method Man page
ISA Man page
ISA2heatmap Man page
ISACHR Man page
ISAEnrichment Man page
ISAExpressionSet Man page
ISAExpressionSet-class Man page
ISAFilterRobust Man page
ISAGO Man page
ISAHTML Man page
ISAHTMLModules Man page
ISAHTMLTable Man page
ISAIterate Man page
ISAKEGG Man page
ISAmiRNA Man page
ISAmnplot Man page
ISAModules Man page
[,ISAModules,ANY,ANY,ANY-method Man page
[,ISAModules,ANY,ANY-method Man page
[[,ISAModules,ANY,ANY-method Man page
[,ISAModules,ANY-method Man page
[[,ISAModules,ANY-method Man page
ISAModules-class Man page
ISANormalize Man page
ISARobustness Man page
ISASweep Man page
ISASweepGraph Man page
ISASweepGraphPlot Man page
ISAUnique Man page
KEGGListHyperGParams Man page
KEGGListHyperGParams-class Man page
KEGGListHyperGResult Man page
KEGGListHyperGResult-class Man page
length,ISAModules-method Man page
ListHyperGParams Man page
ListHyperGParams-class Man page
ListHyperGResult Man page
ListHyperGResult-class Man page
makeValidParams,CHRListHyperGParams-method Man page
makeValidParams,GeneralListHyperGParams-method Man page
makeValidParams,GOListHyperGParams-method Man page
makeValidParams,KEGGListHyperGParams-method Man page
makeValidParams,ListHyperGParams-method Man page
makeValidParams,miRNAListHyperGParams-method Man page
miRNAListHyperGParams Man page
miRNAListHyperGParams-class Man page
miRNAListHyperGResult Man page
miRNAListHyperGResult-class Man page
mnplot Man page
oddsRatios,CHRListHyperGResult-method Man page
oddsRatios,GeneralListHyperGResult-method Man page
oddsRatios,GOListHyperGResult-method Man page
oddsRatios,KEGGListHyperGResult-method Man page
oddsRatios,ListHyperGResult-method Man page
oddsRatios,miRNAListHyperGResult-method Man page
ontology<-,GOListHyperGParams,character-method Man page
ontology,GOListHyperGParams-method Man page
ontology,GOListHyperGResult-method Man page
overlap Man page
overlapPlot Man page
pData,ISAModules-method Man page
prenormalized Man page
prenormalized<- Man page
prenormalized<-,ISAExpressionSet-method Man page
prenormalized,ISAExpressionSet-method Man page
print.ISAexpPlot Man page
profilePlot Man page
pvalues,CHRListHyperGResult-method Man page
pvalues,GeneralListHyperGResult-method Man page
pvalues,GOListHyperGResult-method Man page
pvalues,KEGGListHyperGResult-method Man page
pvalues,ListHyperGResult-method Man page
pvalues,miRNAListHyperGResult-method Man page
runData Man page
runData,ISAModules-method Man page
sampExprs Man page
sampExprs,ISAExpressionSet-method Man page
sampleNames,ISAModules-method Man page
sampleThreshold Man page
sampleThreshold,ISAModules-method Man page
seedData Man page
seedData,ISAModules-method Man page
sigCategories,CHRListHyperGResult-method Man page
sigCategories,GeneralListHyperGResult-method Man page
sigCategories,GOListHyperGResult-method Man page
sigCategories,KEGGListHyperGResult-method Man page
sigCategories,ListHyperGResult-method Man page
sigCategories,miRNAListHyperGResult-method Man page
summary,CHRListHyperGResult-method Man page
summary,GeneralListHyperGResult-method Man page
summary,GOListHyperGResult-method Man page
summary,KEGGListHyperGResult-method Man page
summary,ListHyperGResult-method Man page
summary,miRNAListHyperGResult-method Man page
universeCounts,CHRListHyperGResult-method Man page
universeCounts,GeneralListHyperGResult-method Man page
universeCounts,GOListHyperGResult-method Man page
universeCounts,KEGGListHyperGResult-method Man page
universeCounts,ListHyperGResult-method Man page
universeCounts,miRNAListHyperGResult-method Man page
universeMappedCount,CHRListHyperGResult-method Man page
universeMappedCount,GeneralListHyperGResult-method Man page
universeMappedCount,GOListHyperGResult-method Man page
universeMappedCount,KEGGListHyperGResult-method Man page
universeMappedCount,ListHyperGResult-method Man page
universeMappedCount,miRNAListHyperGResult-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/CHR.R R/GO.R R/ISAExpressionSet-methods.R R/ISAModules-methods.R R/KEGG.R R/autil.R R/autogen.R R/biclust.R R/eisa.R R/enrichment.R R/generalenrichment.R R/miRNA.R R/viz.R R/zzz.R
build
build/vignette.rds
data
data/ALLModules.rda
data/ALLModulesSmall.rda
inst
inst/CITATION
inst/autogen
inst/autogen/images
inst/autogen/images/CBG_clip_image001_small.jpg
inst/autogen/images/colbar.png
inst/autogen/images/color1.png
inst/autogen/images/color10.png
inst/autogen/images/color11.png
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inst/autogen/images/color26.png
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inst/autogen/images/color4.png
inst/autogen/images/color5.png
inst/autogen/images/color6.png
inst/autogen/images/color7.png
inst/autogen/images/color8.png
inst/autogen/images/color9.png
inst/autogen/images/firefox.png
inst/autogen/images/headerbg.png
inst/autogen/images/point-hover.png
inst/autogen/images/point-hover2.png
inst/autogen/images/sib_logo_home.png
inst/autogen/images/valid-xhtml11-blue.png
inst/autogen/images/vcss-blue.png
inst/autogen/mainlattice.html.in
inst/autogen/mainlattice.js
inst/autogen/maintable.html.in
inst/autogen/maintree.html.in
inst/autogen/maintree.js
inst/autogen/mapevents.js
inst/autogen/module.html.in
inst/autogen/module.js.in
inst/autogen/style-lattice.css.in
inst/autogen/style-mod.css.in
inst/autogen/style-table.css
inst/autogen/style.css.in
inst/doc
inst/doc/EISA_tutorial.R
inst/doc/EISA_tutorial.Rnw
inst/doc/EISA_tutorial.pdf
man
man/ALLModules.Rd man/ISA.CHR.Rd man/ISA.GO.Rd man/ISA.KEGG.Rd man/ISA.Rd man/ISA.html.Rd man/ISA.iterate.Rd man/ISA.miRNA.Rd man/ISA.normalize.Rd man/ISA.sweep.Rd man/ISA.unique.Rd man/ISA2heatmap.Rd man/ISAExpressionSet.Rd man/ISAModules-class.Rd man/ListHyperGParams-class.Rd man/ListHyperGResult-class.Rd man/cond.plot.Rd man/eisa.biclust.Rd man/enrichment.Rd man/exp.plot.Rd man/gograph.Rd man/mnplot.Rd man/overlap.Rd man/profilePlot.Rd man/robustness.Rd
vignettes
vignettes/EISA.bib
vignettes/EISA_biclust.pdf
vignettes/EISA_biclust.vignette
vignettes/EISA_tutorial.Rnw
vignettes/ISA_internals.pdf
vignettes/ISA_internals.vignette
vignettes/plot-HTMLTable.png
vignettes/tissues.pdf
vignettes/tissues.vignette

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