Learn R Programming

eisa (version 1.24.0)

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.

Copy Link

Version

Version

1.24.0

License

GPL (>= 2)

Maintainer

Gabor Csardi

Last Published

February 15th, 2017

Functions in eisa (1.24.0)

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