Package: attract 1.65.0

Samuel Zimmerman

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.

Authors:Jessica Mar

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card.svg |card.png
attract/json (API)
NEWS

# Install 'attract' in R:
install.packages('attract', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • exprs.dat - Gene Expression Matrix of Published Data
  • loring.eset - An ExpressionSet Object containing published data from M?ller et al.
  • samp.info - Samp.info Contains the Sample Information for the Mueller data set.
  • subset.loring.eset - An ExpressionSet Object containing published data from M?ller et al.

On BioConductor:attract-1.65.0(bioc 3.24)attract-1.64.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologykeggreactomegeneexpressionpathwaysgenesetenrichmentmicroarrayrnaseq

3.30 score 4 scripts 600 downloads 1 mentions 7 exports 60 dependencies

Last updated from:3c63287504. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

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bioc-checksERROR264
linux-devel-x86_64NOTE480
source / vignettesOK418
linux-release-x86_64NOTE428
macos-release-arm64NOTE357
macos-oldrel-arm64NOTE261
windows-develNOTE401
windows-releaseNOTE348
windows-oldrelNOTE384
wasm-releaseOK218

Exports:calcFuncSynexprsfilterDataSetfindAttractorsfindCorrPartnersfindSynexprsplotsynexprsremoveFlatGenes

Dependencies:annotateAnnotationDbiAnnotationForgeaskpassBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemCategorycliclustercpp11crayoncurlDBIfastmapgenefiltergenericsglueGO.dbGOstatsgraphGSEABasehttrIRangesjsonliteKEGGRESTlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigpngR6RBGLRCurlreactome.dbRgraphvizrlangRSQLiteS4VectorsSeqinfostatmodsurvivalsysvctrsXMLxtableXVector

Tutorial on How to Use the Functions in the \texttt{attract} Package

Rendered fromattract.Rnwusingutils::Sweaveon May 30 2026.

Last update: 2016-05-23
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Methods to find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscapeattract-package attract
Class AttractorModuleSetAttractorModuleSet AttractorModuleSet-class
This function builds an incidence matrix for custom gene sets.buildCustomIncidenceMatrix
Functional enrichmental analysis for a set of synexpression groups.calcFuncSynexprs
Function calculates the informativeness metric (average MSS) for a set of cluster assignments.calcInform
Function calculates a modified F-statistic for a set of cluster assignments.calcModfstat
Function calculates the average RSS for a set of cluster assignments.calcRss
Gene Expression Matrix of Published Dataexprs.dat
This function filters our lowly expressed genes in RNAseq data.filterDataSet
Infers the set of cell-lineage specific gene expression modules using GSEAlm and KEGG.findAttractors
Determines Genes with Highly Correlated Expression Profiles to a Synexpression GroupfindCorrPartners
This function finds the synexpression groups present within a core attractor pathway module.findSynexprs
An ExpressionSet Object containing published data from M?ller et al.loring.eset
Visualizing the Average Expression Profile of a Synexpression Group.plotsynexprs
Flags a set of genes which demonstrates little variation across the celltypes or experimental groups of interest.removeFlatGenes
samp.info Contains the Sample Information for the Mueller data set.samp.info
An ExpressionSet Object containing published data from M?ller et al.subset.loring.eset
Class SynExpressionSetSynExpressionSet SynExpressionSet-class