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rTRM (version 1.10.2)

Identification of transcriptional regulatory modules from PPI networks

Description

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

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Version

Version

1.10.2

License

GPL-3

Issues

0

Pull Requests

0

Stars

3

Forks

2

Maintainer

Diego Diez

Last Published

February 15th, 2017

Functions in rTRM (1.10.2)

getAnnotations

Obtain the 'pwm' table fromt the database, containing PWM's annotations.
annotateTRM

Annotate a network object with information about clusters.
getMaps

Obtain the mapping between PWM and Entrez Gene identifiers.
getMotifsFromEntrezgene

Retrieve PWMs associated with genes provided as entrezgene identifiers.
plotGraph

Plot an graph in igraph format.
plotDegree

Plot degree distribution for network nodes
layout.concentric

Generates a concentric layout for graphs
getMatrices

Obtain a list of PWMs.
getSequencesFromGenome

Retrieves a set of sequences from a BSgenome object and optionally appends a label to each sequence id.
getTFterms

Get terms associated with a specified TFclass subset.
plotTRMlegend

Plot the legend of a TRM with information about the cluster families.
plotTRM

Plot an annotated TRM.
biogrid_hs

Network dataset of class 'igraph'
getBiogridData

Downloads network data from BioGRID in TAB2 format.
annotateFreq

Annotate a graph with frequency of nodes/edges in other graphs.
findTRM

Indentifies a TRM associated with a target node and one or more query nodes.
getLargestComp

Gets the largest connected component
rTRMui-package

rTRM shiny UI
getOrthologs

Obtain the mapping to Entrez Gene identifiers in the given organism.
getSimilarityMatrix

Compute similarity matrix of list of graphs.
writeTRMreport

Export a table with TRM nodes and associated information.
getMotifsFromSymbol

Retrieve PWMs associated with genes provided as symbol.
getOrthologsFromBiomart

Returns ortholog genes for a target organism
biogrid_mm

Network dataset of class 'igraph'
initBiomart

Initializes mart objects to identify ortholog genes
removeVertices

Remove nodes from a graph and returns the largest component
annotateModule

Annotate a network module with information
processBiogrid

Process a data.frame with BioGRID data into a network for a target organism
getConcentricList

Returns a list with nodes membership to be used in a graph with a concentric layout
layout.arc

Layouts a graph using arcs.
runTRM

Runs an rTRM (shiny) web server.
getOrthologFromMatrix

Obtain gene identifiers for a target organism associated with a list of PWMs.
getTFclass

Return the ontology in the TFclass database associated with an entrezgene identifier
rTRM-package

Identification transcription regulatory modules (TRMs)
getTFclassFromEntrezgene

Applies getTFclass sequentially to a vector of entrezgene identifiers.