RankProd pipeline

RankProd specifications

Information


Unique identifier OMICS_01313
Name RankProd
Alternative name RankProd 2.0
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 3.3.4
Stability Beta
Requirements stats, methods, Rmpfr, gmp
Maintained Yes

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Maintainers


  • person_outline Rainer Breitling <>
  • person_outline Francesco Del Carratore <>
  • person_outline Andris Jankevics <>
  • person_outline Fangxin Hong <>
  • person_outline Ben Wittner <>

Publications for RankProd

RankProd IN pipelines

 (4)
2017
PMCID: 5436525
PMID: 28529649
DOI: 10.7150/thno.18415

[…] data are available from the gene expression omnibus (geo) repository, accession number gse88964., an expression matrix was processed for differential expression by employing the rank product method (rankprod) with the rankprod package in r. the differentially expressed genes were analyzed by web-based gene set analysis toolkit (webgestalt) for gene ontology (go) enrichment, kyoto encyclopedia […]

2017
PMCID: 5436525
PMID: 28529649
DOI: 10.7150/thno.18415

[…] from the gene expression omnibus (geo) repository, accession number gse88964., an expression matrix was processed for differential expression by employing the rank product method (rankprod) with the rankprod package in r. the differentially expressed genes were analyzed by web-based gene set analysis toolkit (webgestalt) for gene ontology (go) enrichment, kyoto encyclopedia of genes and genomes […]

2015
PMCID: 4517500
PMID: 26215595
DOI: 10.1186/s12870-015-0568-4

[…] and sub-network 6 included two probe sets for lectin-related proteins., using wgcna package [33], we constructed a weighted co-expression network of the 3,499 probe sets identified by both limma and rankprod. this network has helped to elucidate tightly co-expressed modules and to identify hub probe sets in the respective modules [33, 46]. our network construction yielded 2,071 nodes and 134,217 […]

2015
PMCID: 4665311
PMID: 26788135
DOI: 10.3892/ol.2015.3761

[…] bayesian approach and the search tool for the retrieval of interacting genes/proteins database, based on the differentially-expressed (de) genes in pediatric all, which were identified using the rankprod package. enrichment analysis of the interaction network was performed using the network-based methods enrichnet and pathexpand, which were compared with the traditional expression analysis […]

RankProd institution(s)
Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK; Department of Electrical Engineering and Electronics, University of Liverpool, Liverpool, UK; Department of Social Science Research Methods, Radboud University Nijmegen, Nijmegen, Netherlands; Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, Netherlands; Harvard School of Public Health, Dana-Farber Cancer Institute, Boston, MA, USA
RankProd funding source(s)
Supported by the BBSRC [BB/M017702/1]; “Centre for synthetic biology of fine and speciality chemicals”.

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