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eisa (version 1.18.0)

Expression data analysis via the Iterative Signature Algorithm

Description

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.

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Version

Version

1.18.0

License

GPL (>= 2)

Maintainer

Gabor Csardi

Last Published

February 15th, 2017

Functions in eisa (1.18.0)

Calculate chromosome enrichment for transcription modules

Calculate (predicted) miRNA target enrichment for transcription modules

Calculate Gene Ontology enrichment for transcription modules

ISAFilterRobust

Robustness of ISA biclusters

Normalize expression data for the Iterative Signature Algorithm

Calculate KEGG Pathway enrichment for transcription modules

Iterative Signature Algorithm on Gene Expression data

Plot part of the Gene Ontology hierarchy

Expression matrix plots for ISA modules

Create an ISA module tree

Remove duplicated ISA modules

Overlap of ISA biclusters

Profile plots for ISA biclusters

ISA-Biclust conversion

Convert ISA modules to a Biclust object, or the opposite

Enrichment analysis for transcription modules, based on user-defined categories

ISAModules-class

A set of ISA modules

ListHyperGParams-class

Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation of multiple gene sets.

ListHyperGResult-class

Classes for quick GO/KEGG/CHR/miRNA target or other enrichment calculation for multiple gene sets

Plot group means against each other, for an ISA module

Create HTML summary pages from the result of modular analysis

Perform the Iterative Signature Algorithm

Heatmap of a transcription module

ISAExpressionSet-class

Expression Set, normalized for using with ISA

ISA transcription modules for the ALL data

Plot sample scores of a transcription module