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RankProd specifications


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
methods, stats, graphics, R(>=3.2.1), Rmpfr, gmp
Maintained Yes




No version available



  • 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 citations


System wide coordinates of higher order functions in host pathogen environment upon Mycobacterium tuberculosis infection

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

[…] nes 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 which […]


Metabolomic analysis of tomato seed germination

PMCID: 5653705
PMID: 29104520
DOI: 10.1007/s11306-017-1284-x

[…] Metabolomics data were log2 transformed and then statistically analyzed using the rank product method (Breitling et al. ) to identify differentially changed metabolites with the Bioconductor ‘RankProd’ package. Significantly changed metabolites showed a false discovery rate (FDR) < 0.05. The FDR value in the rank product was obtained with 1000 random permutations. Principal component analy […]


Gene expression profiling of hepatocarcinogenesis in a mouse model of chronic hepatitis B

PLoS One
PMCID: 5624708
PMID: 28968425
DOI: 10.1371/journal.pone.0185442

[…] chronological sample in the unmanipulated control Tg mix, two color microarray analysis was performed by setting the samples with log2 ratios of 0. False Discovery Rate (FDR) with Welch P-values and RankProd FDR were respectively corrected for multiple testing with Benjamin-Hochberg (BH) procedure and RankProduct. While Welch P-values were calculated from TM4 MeV_4_6_1, R was used for RankProduct […]


Transcriptome analysis uncovers Arabidopsis F BOX STRESS INDUCED 1 as a regulator of jasmonic acid and abscisic acid stress gene expression

BMC Genomics
PMCID: 5512810
PMID: 28716048
DOI: 10.1186/s12864-017-3864-6

[…] .edu/facility/genomics.html) according to standard Affymetrix protocols (Affymetrix | Thermo Fisher Scientific, www.thermofisher.com). The .CEL files were analyzed in R using the Bioconductor package RankProd []. Prior to processing, chips were normalized in R using Robust Multi-Array (RMA) normalization. Pearson correlation co-efficient (r) values between all independent biological replicate comp […]


A novel plant E3 ligase stabilizes Escherichia coli heat shock factor σ32

Sci Rep
PMCID: 5481349
PMID: 28642478
DOI: 10.1038/s41598-017-03056-6

[…] iscovery rate (FDR) <0.05 for the t-test and U-test, together with fold-change cut-off values of 2.0-fold decrease and increase. Two more sophisticated methods in R/Bioconductor packages “Limma” and “RankProd” were used (Supplementary Table ). The intersection of DEGs identified using the five methods were considered to be significantly up- or down-regulated in BnTR1 strains at 37 °C and 42 °C, re […]


Folate deficiency disturbs hsa‐let‐7 g level through methylation regulation in neural tube defects

J Cell Mol Med
PMCID: 5706510
PMID: 28631291
DOI: 10.1111/jcmm.13228

[…] ch has over 47,000 probes for assessing mRNA expression, was selected to generate whole‐genome mRNA expression profiles for both NTD‐affected and normal tissue samples. DEGs were identified using the RankProd program , which uses a nonparametric statistical method to estimate significance levels of genes' differential expression (rank) based on a gene permutation model. For the multitest correctio […]


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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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