RankProd protocols

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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 3.7.0
Stability Beta
Requirements
methods, stats, graphics, R(>=3.2.1), 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

 (18)
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 […]

2016
PMCID: 5143378
PMID: 27253413
DOI: 10.1038/cddis.2016.148

[…] transformed ratios of polysomal over subpolysomal signal were then subjected to a panel of four different statistical approaches: (1) « limma » based on model fitting in the limma package; (2) « rankprod » based on ranking analysis in the rankprod package;, (3) « sam » based on non-parametric approach; (4) and « t-test » based on a basic student's t-test. genes identified as significantly […]

2015
PMCID: 4334673
PMID: 25491268
DOI: 10.1111/febs.13172

[…] (gse13009 for parental mcf-7 cells and gse57547 for 6kr cells). genes for which the expression levels were altered relative to the nontreated cells after growth factor treatment were extracted using rankprod (fdr < 0.01). time- and ligand-dependent expression profiles of differentially expressed genes were analyzed by hierarchical clustering using pvclust (clustering method: average linkage, […]

2015
PMCID: 4430867
PMID: 25948104
DOI: 10.1186/s12885-015-1337-3

[…] studies, where we could not run rmaexpress quality control, we downloaded already normalized, _raw.tar files and used these without further modifications, as submitted by the original authors., rankprod package analyses gene expression microarray data specifically to identify differentially expressed genes. rankprod uses non-parametric rank product method to detect genes […]

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 [], 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 [, ]. our network construction yielded 2,071 nodes and 134,217 […]


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RankProd in publications

 (200)
PMCID: 5934403
PMID: 29725010
DOI: 10.1038/s41467-018-04150-7

[…] processed in the r environment. normalization was obtained with the lumi package, and differential analysis was performed by applying a permutation-based non-parametric method implemented in the rankprod package. differential expressed genes were selected according to the threshold fdr q-value < 0.05., statistical analysis using a 2-tailed unpaired student’s t test or 2-way anova […]

PMCID: 5911478
PMID: 29713312
DOI: 10.3389/fendo.2018.00158

[…] and pathways in cancer (p = 2.48e−02)., in order to analyze the 3p and 5p expression ratio on the same mirna in two different groups, ptc lnm-p and ptc lnn tumor sequencing data were analyzed using rankprod (). ninety-six mirna had significant differential expression ratio and present on both group. table and figure show the list of top 20 mirnas with significant 3p/5p ratio., analysis […]

PMCID: 5899355
PMID: 29653596
DOI: 10.1186/s12920-018-0357-7

[…] with estimating the h2 value for pd, and then identified 17 new pd risk loci. wang q et al. [] performed a meta-analysis with 9 microarray datasets of pd studies in every brain region using the rankprod method []., our meta-analysis was conducted on pd patients and healthy controls microarray datasets obtained from the sn brain region and blood using vote counting generic ways. […]

PMCID: 5864717
PMID: 29567998
DOI: 10.1038/s41598-018-22884-8

[…] during infection, we considered the samples during the final stage of the infection. differential expression analysis of gene expression microarray data was carried out using an r package called ‘rankprod’. the package uses a modified ‘rank product’ method, to identify up or down-regulated genes in one condition against another. we have used rankprod because, it uses rank product method […]

PMCID: 5901021
PMID: 29461643
DOI: 10.1002/ana.25187

[…] performed background correction, summarization, and normalization using the rma function in the bioconductor package. we compared microrna expression in tissues with fcd type ii and controls using rankprod (bioconductor package) software and false discovery rate correction for multiple comparisons. micrornas were considered differentially expressed when the fold change (fc) was greater […]


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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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