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

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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.

Author
Jessica Mar
Date of publication
None
Maintainer
Samuel Zimmerman <sezimmer@einstein.yu.edu>
License
LGPL (>= 2.0)
Version
1.26.0

View on Bioconductor

Man pages

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

Files in this package

attract/DESCRIPTION
attract/NAMESPACE
attract/NEWS
attract/R
attract/R/classdef.R
attract/R/findAttractorsStep.R
attract/R/findFuncEnrichAndCorr.R
attract/R/findSynexprsStep.R
attract/R/removeFlatGenesStep.R
attract/build
attract/build/vignette.rds
attract/data
attract/data/datalist
attract/data/exprs.dat.rda
attract/data/loring.eset.rda
attract/data/samp.info.rda
attract/data/subset.loring.eset.rda
attract/inst
attract/inst/doc
attract/inst/doc/attract.R
attract/inst/doc/attract.Rnw
attract/inst/doc/attract.pdf
attract/inst/extdata
attract/inst/extdata/c4.cgn.v5.0.entrez.gmt
attract/man
attract/man/AttractorModuleSet-class.Rd
attract/man/SynExpressionSet-class.Rd
attract/man/attract-package.Rd
attract/man/buildCorMatrix.Rd
attract/man/buildCustomIncidenceMatrix.Rd
attract/man/buildKeggIncidenceMatrix.Rd
attract/man/calcFuncSynexprs.Rd
attract/man/calcInform.Rd
attract/man/calcModfstat.Rd
attract/man/calcRss.Rd
attract/man/exprs.dat.Rd
attract/man/filterDataSet.Rd
attract/man/findAttractors.Rd
attract/man/findCorrPartners.Rd
attract/man/findOnepwaySynexprs.Rd
attract/man/findSynexprs.Rd
attract/man/flagPwayExists.Rd
attract/man/getCustomGenes.Rd
attract/man/getPwayGenes.Rd
attract/man/loring.eset.Rd
attract/man/plotsynexprs.Rd
attract/man/removeFlatGenes.Rd
attract/man/samp.info.Rd
attract/man/subset.loring.eset.Rd
attract/vignettes
attract/vignettes/attract.Rnw
attract/vignettes/fancyvrb.sty