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.

Author
Gabor Csardi <csardi.gabor@gmail.com>
Date of publication
None
Maintainer
Gabor Csardi <csardi.gabor@gmail.com>
License
GPL (>= 2)
Version
1.26.0

View on Bioconductor

Man pages

ALLModules
ISA transcription modules for the ALL data
cond.plot
Plot sample scores of a transcription module
eisa.biclust
Convert ISA modules to a Biclust object, or the opposite
enrichment
Enrichment analysis for transcription modules, based on...
exp.plot
Expression matrix plots for ISA modules
gograph
Plot part of the Gene Ontology hierarchy
ISA
Iterative Signature Algorithm on Gene Expression data
ISA2heatmap
Heatmap of a transcription module
ISA.CHR
Calculate chromosome enrichment for transcription modules
ISAExpressionSet
Expression Set, normalized for using with ISA
ISA.GO
Calculate Gene Ontology enrichment for transcription modules
ISA.html
Create HTML summary pages from the result of modular analysis
ISA.iterate
Perform the Iterative Signature Algorithm
ISA.KEGG
Calculate KEGG Pathway enrichment for transcription modules
ISA.miRNA
Calculate (predicted) miRNA target enrichment for...
ISAModules-class
A set of ISA modules
ISA.normalize
Normalize expression data for the Iterative Signature...
ISA.sweep
Create an ISA module tree
ISA.unique
Remove duplicated ISA modules
ListHyperGParams-class
Classes for quick GO/KEGG/CHR/miRNA target or other...
ListHyperGResult-class
Classes for quick GO/KEGG/CHR/miRNA target or other...
mnplot
Plot group means against each other, for an ISA module
overlap
Overlap of ISA biclusters
profilePlot
Profile plots for ISA biclusters
robustness
Robustness of ISA biclusters

Files in this package

eisa/DESCRIPTION
eisa/NAMESPACE
eisa/R
eisa/R/AllClasses.R
eisa/R/AllGenerics.R
eisa/R/CHR.R
eisa/R/GO.R
eisa/R/ISAExpressionSet-methods.R
eisa/R/ISAModules-methods.R
eisa/R/KEGG.R
eisa/R/autil.R
eisa/R/autogen.R
eisa/R/biclust.R
eisa/R/eisa.R
eisa/R/enrichment.R
eisa/R/generalenrichment.R
eisa/R/miRNA.R
eisa/R/viz.R
eisa/R/zzz.R
eisa/build
eisa/build/vignette.rds
eisa/data
eisa/data/ALLModules.rda
eisa/data/ALLModulesSmall.rda
eisa/inst
eisa/inst/CITATION
eisa/inst/autogen
eisa/inst/autogen/images
eisa/inst/autogen/images/CBG_clip_image001_small.jpg
eisa/inst/autogen/images/colbar.png
eisa/inst/autogen/images/color1.png
eisa/inst/autogen/images/color10.png
eisa/inst/autogen/images/color11.png
eisa/inst/autogen/images/color12.png
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eisa/inst/autogen/images/color15.png
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eisa/inst/autogen/images/color18.png
eisa/inst/autogen/images/color19.png
eisa/inst/autogen/images/color2.png
eisa/inst/autogen/images/color20.png
eisa/inst/autogen/images/color21.png
eisa/inst/autogen/images/color22.png
eisa/inst/autogen/images/color23.png
eisa/inst/autogen/images/color24.png
eisa/inst/autogen/images/color25.png
eisa/inst/autogen/images/color26.png
eisa/inst/autogen/images/color27.png
eisa/inst/autogen/images/color28.png
eisa/inst/autogen/images/color29.png
eisa/inst/autogen/images/color3.png
eisa/inst/autogen/images/color30.png
eisa/inst/autogen/images/color31.png
eisa/inst/autogen/images/color4.png
eisa/inst/autogen/images/color5.png
eisa/inst/autogen/images/color6.png
eisa/inst/autogen/images/color7.png
eisa/inst/autogen/images/color8.png
eisa/inst/autogen/images/color9.png
eisa/inst/autogen/images/firefox.png
eisa/inst/autogen/images/headerbg.png
eisa/inst/autogen/images/point-hover.png
eisa/inst/autogen/images/point-hover2.png
eisa/inst/autogen/images/sib_logo_home.png
eisa/inst/autogen/images/valid-xhtml11-blue.png
eisa/inst/autogen/images/vcss-blue.png
eisa/inst/autogen/mainlattice.html.in
eisa/inst/autogen/mainlattice.js
eisa/inst/autogen/maintable.html.in
eisa/inst/autogen/maintree.html.in
eisa/inst/autogen/maintree.js
eisa/inst/autogen/mapevents.js
eisa/inst/autogen/module.html.in
eisa/inst/autogen/module.js.in
eisa/inst/autogen/style-lattice.css.in
eisa/inst/autogen/style-mod.css.in
eisa/inst/autogen/style-table.css
eisa/inst/autogen/style.css.in
eisa/inst/doc
eisa/inst/doc/EISA_tutorial.R
eisa/inst/doc/EISA_tutorial.Rnw
eisa/inst/doc/EISA_tutorial.pdf
eisa/man
eisa/man/ALLModules.Rd
eisa/man/ISA.CHR.Rd
eisa/man/ISA.GO.Rd
eisa/man/ISA.KEGG.Rd
eisa/man/ISA.Rd
eisa/man/ISA.html.Rd
eisa/man/ISA.iterate.Rd
eisa/man/ISA.miRNA.Rd
eisa/man/ISA.normalize.Rd
eisa/man/ISA.sweep.Rd
eisa/man/ISA.unique.Rd
eisa/man/ISA2heatmap.Rd
eisa/man/ISAExpressionSet.Rd
eisa/man/ISAModules-class.Rd
eisa/man/ListHyperGParams-class.Rd
eisa/man/ListHyperGResult-class.Rd
eisa/man/cond.plot.Rd
eisa/man/eisa.biclust.Rd
eisa/man/enrichment.Rd
eisa/man/exp.plot.Rd
eisa/man/gograph.Rd
eisa/man/mnplot.Rd
eisa/man/overlap.Rd
eisa/man/profilePlot.Rd
eisa/man/robustness.Rd
eisa/vignettes
eisa/vignettes/EISA.bib
eisa/vignettes/EISA_biclust.pdf
eisa/vignettes/EISA_biclust.vignette
eisa/vignettes/EISA_tutorial.Rnw
eisa/vignettes/ISA_internals.pdf
eisa/vignettes/ISA_internals.vignette
eisa/vignettes/plot-HTMLTable.png
eisa/vignettes/tissues.pdf
eisa/vignettes/tissues.vignette