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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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 in publications

 (2)
PMCID: 5787480
PMID: 29416627
DOI: 10.18632/oncotarget.23065

[…] 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 []., all together 1,988 cancer samples measured by illumina gene chips published in the metabric project were obtained […]

PMCID: 5180091
PMID: 28008934
DOI: 10.1038/srep38988

[…] 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., an effort was made to reduce feature redundancy by avoiding the use of multiple data sources for the same feature type. for example, we did not use pathway data […]


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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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