attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

This package contains the functions to find the gene expression modules that represent the drivers of Kauffman's attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.

AuthorJessica Mar
Date of publicationNone
MaintainerSamuel Zimmerman <sezimmer@einstein.yu.edu>
LicenseLGPL (>= 2.0)
Version1.26.0

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AttractorModuleSet-class: Class AttractorModuleSet

attract-package: Methods to find the Gene Expression Modules that Represent...

buildCorMatrix: Internal function - builds the correlation matrix between an...

buildCustomIncidenceMatrix: This function builds an incidence matrix for custom gene...

buildKeggIncidenceMatrix: Internal function - buildings the KEGG incidence matrix...

calcFuncSynexprs: Functional enrichmental analysis for a set of synexpression...

calcInform: Function calculates the informativeness metric (average MSS)...

calcModfstat: Function calculates a modified F-statistic for a set of...

calcRss: Function calculates the average RSS for a set of cluster...

exprs.dat: Gene Expression Matrix of Published Data

filterDataSet: This function filters our lowly expressed genes in RNAseq...

findAttractors: Infers the set of cell-lineage specific gene expression...

findCorrPartners: Determines Genes with Highly Correlated Expression Profiles...

findOnepwaySynexprs: Internal function - finds the synexpression groups for a...

findSynexprs: This function finds the synexpression groups present within a...

flagPwayExists: Internal function - flags a gene if it exists in a pathway.

getCustomGenes: Function removes genes from the custom pathway that...

getPwayGenes: Function removes genes from the chosen pathway that...

loring.eset: An ExpressionSet Object containing published data from M?ller...

plotsynexprs: Visualizing the Average Expression Profile of a Synexpression...

removeFlatGenes: Flags a set of genes which demonstrates little variation...

samp.info: samp.info Contains the Sample Information for the Mueller...

subset.loring.eset: An ExpressionSet Object containing published data from M?ller...

SynExpressionSet-class: Class SynExpressionSet

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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