rTRM: Identification of transcriptional regulatory modules from PPI networks

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

AuthorDiego Diez
Date of publicationNone
MaintainerDiego Diez <diego10ruiz@gmail.com>
LicenseGPL-3
Version1.12.0
https://github.com/ddiez/rTRM

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.

Functions

annotateFreq Man page
annotateModule Man page
annotateTRM Man page
biogrid_hs Man page
biogrid_mm Man page
findTRM Man page
getAnnotations Man page
getBiogridData Man page
getConcentricList Man page
getLargestComp Man page
getMaps Man page
getMatrices Man page
getMotifsFromEntrezgene Man page
getMotifsFromSymbol Man page
getOrthologFromMatrix Man page
getOrthologs Man page
getOrthologsFromBiomart Man page
getSequencesFromGenome Man page
getSimilarityMatrix Man page
getTFclass Man page
getTFclassFromEntrezgene Man page
getTFterms Man page
initBiomart Man page
layout.arc Man page
layout.concentric Man page
plotDegree Man page
plotGraph Man page
plotTRM Man page
plotTRMlegend Man page
processBiogrid Man page
removeVertices Man page
rTRM Man page
rTRM-package Man page
writeTRMreport Man page

Files

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

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