eisa v1.24.0

by Gabor Csardi

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.

Functions in eisa

Name Description
ISAIterate Perform the Iterative Signature Algorithm
gograph Plot part of the Gene Ontology hierarchy
ISANormalize Normalize expression data for the Iterative Signature Algorithm
ISA-Biclust conversion Convert ISA modules to a Biclust object, or the opposite
ISAGO Calculate Gene Ontology enrichment for transcription modules
profilePlot Profile plots for ISA biclusters
ISAKEGG Calculate KEGG Pathway enrichment for transcription modules
condPlot Plot sample scores of a transcription module
ISA Iterative Signature Algorithm on Gene Expression data
ISAModules-class A set of ISA modules
overlap Overlap of ISA biclusters
ALLModules ISA transcription modules for the ALL data
ISACHR Calculate chromosome enrichment for transcription modules
ListHyperGParams-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.
ISASweep Create an ISA module tree
ISAmiRNA Calculate (predicted) miRNA target enrichment for transcription modules
ISAUnique Remove duplicated ISA modules
ISAFilterRobust Robustness of ISA biclusters
expPlot Expression matrix plots for ISA modules
ISAHTML Create HTML summary pages from the result of modular analysis
mnplot Plot group means against each other, for an ISA module
ISAExpressionSet-class Expression Set, normalized for using with ISA
enrichment Enrichment analysis for transcription modules, based on user-defined categories
ListHyperGResult-class Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets
ISA2heatmap Heatmap of a transcription module
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Details

Date 2014-03-26
License GPL (>= 2)
biocViews Classification, Visualization, Microarray, GeneExpression
Collate AllClasses.R AllGenerics.R ISAExpressionSet-methods.R ISAModules-methods.R enrichment.R CHR.R GO.R KEGG.R miRNA.R autil.R autogen.R biclust.R eisa.R viz.R zzz.R generalenrichment.R

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