Package: attract 1.59.0

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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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-1.59.0(bioc 3.21)attract-1.58.0(bioc 3.20)

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 412 downloads 1 mentions 7 exports 63 dependencies

Last updated 4 months agofrom:33404bad3e. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-winNOTEFeb 17 2025
R-4.5-macNOTEFeb 17 2025
R-4.5-linuxNOTEFeb 17 2025
R-4.4-winNOTEFeb 17 2025
R-4.4-macNOTEFeb 17 2025
R-4.3-winNOTEFeb 17 2025
R-4.3-macNOTEFeb 17 2025

Exports:calcFuncSynexprsfilterDataSetfindAttractorsfindCorrPartnersfindSynexprsplotsynexprsremoveFlatGenes

Dependencies:annotateAnnotationDbiAnnotationForgeaskpassBHBiobaseBiocGenericsBiostringsbitbit64bitopsblobcachemCategorycliclustercpp11crayoncurlDBIfastmapgenefiltergenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbGOstatsgraphGSEABasehttrIRangesjsonliteKEGGRESTlatticelifecyclelimmaMatrixMatrixGenericsmatrixStatsmemoisemimeopensslorg.Hs.eg.dbpkgconfigplogrpngR6RBGLRCurlreactome.dbRgraphvizrlangRSQLiteS4VectorsstatmodsurvivalsysUCSC.utilsvctrsXMLxtableXVector

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

Rendered fromattract.Rnwusingutils::Sweaveon Feb 17 2025.

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