Package: rTRM 1.45.0

Diego Diez

rTRM: Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks

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

Authors:Diego Diez

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rTRM/json (API)
NEWS

# Install 'rTRM' in R:

install.packages('rTRM', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ddiez/rtrm/issues

Datasets:

biogrid_hs - Network dataset of class 'igraph'
biogrid_mm - Network dataset of class 'igraph'

On BioConductor:rTRM-1.45.0(bioc 3.21)rTRM-1.44.0(bioc 3.20)

transcription network generegulation graphandnetwork bioconductor bioinformatics

4.86 score 3 stars 1 packages 3 scripts 305 downloads 4 mentions 32 exports 43 dependencies

Last updated 2 months agofrom:241c6dba7c. Checks:ERROR: 1 NOTE: 4 OK: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Dec 18 2024
R-4.5-win	NOTE	Dec 18 2024
R-4.5-linux	NOTE	Dec 18 2024
R-4.4-win	NOTE	Dec 18 2024
R-4.4-mac	NOTE	Dec 18 2024
R-4.3-win	OK	Dec 18 2024
R-4.3-mac	OK	Dec 18 2024

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

Dependencies:AnnotationDbi askpass Biobase BiocGenerics Biostrings bit bit64 blob cachem cli cpp11 crayon curl DBI fastmap generics GenomeInfoDb GenomeInfoDbData glue httr igraph IRanges jsonlite KEGGREST lattice lifecycle magrittr Matrix memoise mime openssl pkgconfig plogr png R6 rlang RSQLite S4Vectors sys UCSC.utils vctrs XVector zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

rTRM: an R package for the identification of transcription regulatory modules (TRMs)

Diego Diez

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2021-06-19
Started: 2021-06-19

Citation

Development and contributors

Readme and manuals

Help Manual

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