attract: Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Version 1.28.0

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
Bioconductor views GeneExpression GeneSetEnrichment KEGG Microarray Pathways RNASeq Reactome
Date of publicationNone
MaintainerSamuel Zimmerman <sezimmer@einstein.yu.edu>
LicenseLGPL (>= 2.0)
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("attract")

Getting started

Package overview

Popular man pages

attract-package: Methods to find the Gene Expression Modules that Represent...
buildKeggIncidenceMatrix: Internal function - buildings the KEGG incidence matrix...
calcInform: Function calculates the informativeness metric (average MSS)...
calcModfstat: Function calculates a modified F-statistic for a set of...
findAttractors: Infers the set of cell-lineage specific gene expression...
findOnepwaySynexprs: Internal function - finds the synexpression groups for a...
removeFlatGenes: Flags a set of genes which demonstrates little variation...
See all...

All man pages Function index File listing

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

Functions

AttractorModuleSet Man page
AttractorModuleSet-class Man page
SynExpressionSet Man page
SynExpressionSet-class Man page
attract Man page
attract-package Man page
buildCorMatrix Man page Source code
buildCustomIncidenceMatrix Man page Source code
buildKeggIncidenceMatrix Man page Source code
calcFuncSynexprs Man page Source code
calcInform Man page Source code
calcModfstat Man page Source code
calcRss Man page Source code
exprs.dat Man page
filterDataSet Man page Source code
findAttractors Man page Source code
findCorrPartners Man page Source code
findOnepwaySynexprs Man page Source code
findSynexprs Man page Source code
flagPwayExists Man page Source code
getCustomGenes Man page Source code
getPwayGenes Man page Source code
loring.eset Man page
plotsynexprs Man page Source code
removeFlatGenes Man page Source code
samp.info Man page
subset.loring.eset Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/classdef.R
R/findAttractorsStep.R
R/findFuncEnrichAndCorr.R
R/findSynexprsStep.R
R/removeFlatGenesStep.R
build
build/vignette.rds
data
data/datalist
data/exprs.dat.rda
data/loring.eset.rda
data/samp.info.rda
data/subset.loring.eset.rda
inst
inst/doc
inst/doc/attract.R
inst/doc/attract.Rnw
inst/doc/attract.pdf
inst/extdata
inst/extdata/c4.cgn.v5.0.entrez.gmt
man
man/AttractorModuleSet-class.Rd
man/SynExpressionSet-class.Rd
man/attract-package.Rd
man/buildCorMatrix.Rd
man/buildCustomIncidenceMatrix.Rd
man/buildKeggIncidenceMatrix.Rd
man/calcFuncSynexprs.Rd
man/calcInform.Rd
man/calcModfstat.Rd
man/calcRss.Rd
man/exprs.dat.Rd
man/filterDataSet.Rd
man/findAttractors.Rd
man/findCorrPartners.Rd
man/findOnepwaySynexprs.Rd
man/findSynexprs.Rd
man/flagPwayExists.Rd
man/getCustomGenes.Rd
man/getPwayGenes.Rd
man/loring.eset.Rd
man/plotsynexprs.Rd
man/removeFlatGenes.Rd
man/samp.info.Rd
man/subset.loring.eset.Rd
vignettes
vignettes/attract.Rnw
vignettes/fancyvrb.sty
attract documentation built on May 20, 2017, 10:14 p.m.

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