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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
attract/json (API)

# 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.

immunooncology kegg reactome geneexpression pathways genesetenrichment microarray rnaseq

3.30 score 4 scripts 1 mentions 7 exports 60 dependencies

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

Target	Result	Time
bioc-checks	ERROR	243
linux-devel-x86_64	NOTE	450
source / vignettes	OK	404
linux-release-x86_64	NOTE	459
macos-release-arm64	NOTE	272
macos-oldrel-arm64	NOTE	253
windows-devel	NOTE	295
windows-release	NOTE	385
windows-oldrel	NOTE	346
wasm-release	OK	227

Exports:calcFuncSynexprs filterDataSet findAttractors findCorrPartners findSynexprs plotsynexprs removeFlatGenes

Dependencies:annotate AnnotationDbi AnnotationForge askpass BH Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem Category cli cluster cpp11 crayon curl DBI fastmap genefilter generics glue GO.db GOstats graph GSEABase httr IRanges jsonlite KEGGREST lattice lifecycle limma Matrix MatrixGenerics matrixStats memoise mime openssl org.Hs.eg.db pkgconfig png R6 RBGL RCurl reactome.db Rgraphviz rlang RSQLite S4Vectors Seqinfo statmod survival sys vctrs XML xtable XVector

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

Rendered fromattract.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Methods to find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape	attract-package attract
Class AttractorModuleSet	AttractorModuleSet 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 Data	exprs.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 Group	findCorrPartners
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 SynExpressionSet	SynExpressionSet SynExpressionSet-class