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.

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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