rTRM specifications

Information


Unique identifier OMICS_10662
Name rTRM
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Input data are enriched motifs from ChIP-seq-ed regions and the genes expressed.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Requirements
igraph
Maintained Yes

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Versioning


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Maintainer


  • person_outline Diego Miranda-Saavedra

Information


Unique identifier OMICS_10662
Name rTRM
Interface Web user interface
Restrictions to use None
Input data Input data are enriched motifs from ChIP-seq-ed regions and the genes expressed.
Programming languages R
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Diego Miranda-Saavedra

Publications for rTRM

rTRM citations

 (2)
library_books

Transcriptome evolution from breast epithelial cells to basal like tumors

2017
Oncotarget
PMCID: 5787480
PMID: 29416627
DOI: 10.18632/oncotarget.23065

[…] rmed using GOstats []. Physical protein-protein interactions were obtained from BioGrid latest release. Subnetworks of genes were obtained using the function induced_subgraph implemented in R package rTRM []. Network analysis and visualization were performed using Cytoscape []. […]

library_books

Driver gene classification reveals a substantial overrepresentation of tumor suppressors among very large chromatin regulating proteins

2016
Sci Rep
PMCID: 5180091
PMID: 28008934
DOI: 10.1038/srep38988

[…] v3.0b2a.Betweenness centrality: Betweenness centrality was calculated by running the Brandes algorithm, using the iGraph R package, on the BioGRID PPIs (Release: 3.2.111), which were accessed via the rTRM package for this purpose. […]

rTRM institution(s)
World Premier International (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan; South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, UK

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