rTRM: Identification of transcriptional regulatory modules from PPI networks

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rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

Author
Diego Diez
Date of publication
None
Maintainer
Diego Diez <diego10ruiz@gmail.com>
License
GPL-3
Version
1.12.0
URLs

View on Bioconductor

Man pages

annotateFreq
Annotate a graph with frequency of nodes/edges in other...
annotateModule
Annotate a network module with information
annotateTRM
Annotate a network object with information about clusters.
biogrid_hs
Network dataset of class 'igraph'
biogrid_mm
Network dataset of class 'igraph'
findTRM
Indentifies a TRM associated with a target node and one or...
getAnnotations
Obtain the 'pwm' table fromt the database, containing PWM's...
getBiogridData
Downloads network data from BioGRID in TAB2 format.
getConcentricList
Returns a list with nodes membership to be used in a graph...
getLargestComp
Gets the largest connected component
getMaps
Obtain the mapping between PWM and Entrez Gene identifiers.
getMatrices
Obtain a list of PWMs.
getMotifsFromEntrezgene
Retrieve PWMs associated with genes provided as entrezgene...
getMotifsFromSymbol
Retrieve PWMs associated with genes provided as symbol.
getOrthologFromMatrix
Obtain gene identifiers for a target organism associated with...
getOrthologs
Obtain the mapping to Entrez Gene identifiers in the given...
getOrthologsFromBiomart
Returns ortholog genes for a target organism
getSequencesFromGenome
Retrieves a set of sequences from a BSgenome object and...
getSimilarityMatrix
Compute similarity matrix of list of graphs.
getTFclass
Return the ontology in the TFclass database associated with...
getTFclassFromEntrezgene
Applies getTFclass sequentially to a vector of entrezgene...
getTFterms
Get terms associated with a specified TFclass subset.
initBiomart
Initializes mart objects to identify ortholog genes
layout.arc
Layouts a graph using arcs.
layout.concentric
Generates a concentric layout for graphs
plotDegree
Plot degree distribution for network nodes
plotGraph
Plot an graph in igraph format.
plotTRM
Plot an annotated TRM.
plotTRMlegend
Plot the legend of a TRM with information about the cluster...
processBiogrid
Process a data.frame with BioGRID data into a network for a...
removeVertices
Remove nodes from a graph and returns the largest component
rTRM-package
Identification transcription regulatory modules (TRMs)
writeTRMreport
Export a table with TRM nodes and associated information.

Files in this package

rTRM/DESCRIPTION
rTRM/NAMESPACE
rTRM/R
rTRM/R/database.R
rTRM/R/dataset.R
rTRM/R/graph.R
rTRM/R/layout.R
rTRM/R/ortholog.R
rTRM/R/plot.R
rTRM/R/ppi.R
rTRM/R/tfclass.R
rTRM/R/tools.R
rTRM/R/zzz.R
rTRM/build
rTRM/build/rTRM.pdf
rTRM/build/vignette.rds
rTRM/data
rTRM/data/biogrid_hs.rda
rTRM/data/biogrid_mm.rda
rTRM/data/datalist
rTRM/inst
rTRM/inst/CITATION
rTRM/inst/NEWS
rTRM/inst/db
rTRM/inst/db/database.db
rTRM/inst/doc
rTRM/inst/doc/rTRM_Introduction.R
rTRM/inst/doc/rTRM_Introduction.Rnw
rTRM/inst/doc/rTRM_Introduction.pdf
rTRM/inst/extra
rTRM/inst/extra/ESC-expressed.txt
rTRM/inst/extra/ESC_Sox2_peaks.txt
rTRM/inst/extra/example.rda
rTRM/inst/extra/pwm_mm_logn.rda
rTRM/inst/extra/sox2_enr.rda
rTRM/inst/extra/sox2_motif_list.rda
rTRM/inst/extra/test.R
rTRM/inst/unitTests
rTRM/inst/unitTests/test_findTRM.R
rTRM/man
rTRM/man/annotateFreq.Rd
rTRM/man/annotateModule.Rd
rTRM/man/annotateTRM.Rd
rTRM/man/biogrid_hs.Rd
rTRM/man/biogrid_mm.Rd
rTRM/man/findTRM.Rd
rTRM/man/getAnnotations.Rd
rTRM/man/getBiogridData.Rd
rTRM/man/getConcentricList.Rd
rTRM/man/getLargestComp.Rd
rTRM/man/getMaps.Rd
rTRM/man/getMatrices.Rd
rTRM/man/getMotifsFromEntrezgene.Rd
rTRM/man/getMotifsFromSymbol.Rd
rTRM/man/getOrthologFromMatrix.Rd
rTRM/man/getOrthologs.Rd
rTRM/man/getOrthologsFromBiomart.Rd
rTRM/man/getSequencesFromGenome.Rd
rTRM/man/getSimilarityMatrix.Rd
rTRM/man/getTFclass.Rd
rTRM/man/getTFclassFromEntrezgene.Rd
rTRM/man/getTFterms.Rd
rTRM/man/initBiomart.Rd
rTRM/man/layout.arc.Rd
rTRM/man/layout.concentric.Rd
rTRM/man/plotDegree.Rd
rTRM/man/plotGraph.Rd
rTRM/man/plotTRM.Rd
rTRM/man/plotTRMlegend.Rd
rTRM/man/processBiogrid.Rd
rTRM/man/rTRM-package.Rd
rTRM/man/removeVertices.Rd
rTRM/man/writeTRMreport.Rd
rTRM/tests
rTRM/tests/runTests.R
rTRM/vignettes
rTRM/vignettes/rTRM_Introduction.Rnw
rTRM/vignettes/workflow.pdf