rTRM: Identification of transcriptional regulatory modules from PPI networks
Version 1.14.0

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

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AuthorDiego Diez
Bioconductor views GeneRegulation GraphAndNetwork Network Transcription
Date of publicationNone
MaintainerDiego Diez <diego10ruiz@gmail.com>
LicenseGPL-3
Version1.14.0
URL https://github.com/ddiez/rTRM
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("rTRM")

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 Source code
annotateModule Man page Source code
annotateTFclass Source code
annotateTRM Man page Source code
annotateTarget Source code
biogrid_hs Man page Source code
biogrid_mm Man page Source code
checkInNetwork Source code
checkParam Source code
checkValid Source code
dcor Source code
findNeigh Source code
findTRM Man page Source code
floating.pie Source code
getAnnotations Man page Source code
getBiogridData Man page Source code
getConcentricList Man page Source code
getCoordinates Source code
getDefaultDb Source code
getLargestComp Man page Source code
getLegend Source code
getMapFromOrg Source code
getMaps Man page Source code
getMatrices Man page Source code
getMotifsFromEntrezgene Man page Source code
getMotifsFromSymbol Man page Source code
getNiceColors Source code
getNode Source code
getOrthologFromMatrix Man page Source code
getOrthologs Man page Source code
getOrthologsFromBiomart Man page Source code
getSQLresult Source code
getSequencesFromGenome Man page Source code
getSimilarityMatrix Man page Source code
getTFclass Man page Source code
getTFclassColors Source code
getTFclassFromEntrezgene Man page Source code
getTFterms Man page Source code
getTaxidFromOrg Source code
initBiomart Man page Source code
layout.arc Man page Source code
layout.concentric Man page Source code
lum Source code
lum2 Source code
plotDegree Man page Source code
plotGraph Man page Source code
plotTRM Man page Source code
plotTRMlegend Man page Source code
processBiogrid Man page Source code
rTRM Man page
rTRM-package Man page
reduceGraph Source code
removeVertices Man page Source code
writeTRMreport Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/database.R
R/dataset.R
R/graph.R
R/layout.R
R/ortholog.R
R/plot.R
R/ppi.R
R/tfclass.R
R/tools.R
R/zzz.R
build
build/rTRM.pdf
build/vignette.rds
data
data/biogrid_hs.rda
data/biogrid_mm.rda
data/datalist
inst
inst/CITATION
inst/NEWS
inst/db
inst/db/database.db
inst/doc
inst/doc/rTRM_Introduction.R
inst/doc/rTRM_Introduction.Rnw
inst/doc/rTRM_Introduction.pdf
inst/extra
inst/extra/ESC-expressed.txt
inst/extra/ESC_Sox2_peaks.txt
inst/extra/example.rda
inst/extra/pwm_mm_logn.rda
inst/extra/sox2_enr.rda
inst/extra/sox2_motif_list.rda
inst/extra/test.R
inst/unitTests
inst/unitTests/test_findTRM.R
man
man/annotateFreq.Rd
man/annotateModule.Rd
man/annotateTRM.Rd
man/biogrid_hs.Rd
man/biogrid_mm.Rd
man/findTRM.Rd
man/getAnnotations.Rd
man/getBiogridData.Rd
man/getConcentricList.Rd
man/getLargestComp.Rd
man/getMaps.Rd
man/getMatrices.Rd
man/getMotifsFromEntrezgene.Rd
man/getMotifsFromSymbol.Rd
man/getOrthologFromMatrix.Rd
man/getOrthologs.Rd
man/getOrthologsFromBiomart.Rd
man/getSequencesFromGenome.Rd
man/getSimilarityMatrix.Rd
man/getTFclass.Rd
man/getTFclassFromEntrezgene.Rd
man/getTFterms.Rd
man/initBiomart.Rd
man/layout.arc.Rd
man/layout.concentric.Rd
man/plotDegree.Rd
man/plotGraph.Rd
man/plotTRM.Rd
man/plotTRMlegend.Rd
man/processBiogrid.Rd
man/rTRM-package.Rd
man/removeVertices.Rd
man/writeTRMreport.Rd
tests
tests/runTests.R
vignettes
vignettes/rTRM_Introduction.Rnw
vignettes/workflow.pdf
rTRM documentation built on May 20, 2017, 9:43 p.m.