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Protocols

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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Documentation


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 citations

 (202)
library_books

A retinoic acid dependent stroma leukemia crosstalk promotes chronic lymphocytic leukemia progression

2018
Nat Commun
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 […]

library_books

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma

2018
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 […]

library_books

A meta analysis of public microarray data identifies biological regulatory networks in Parkinson’s disease

2018
BMC Med Genomics
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. […]

library_books

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

2018
Sci Rep
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 […]

library_books

Dysregulation of NEUROG2 plays a key role in focal cortical dysplasia

2018
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 […]

library_books

An information theoretic approach to the modeling and analysis of whole genome bisulfite sequencing data

2018
BMC Bioinformatics
PMCID: 5842653
PMID: 29514626
DOI: 10.1186/s12859-018-2086-5

[…] approach (additional file : table s2). we then combined the results of the three comparisons into a single ranked list using the method of rank products [, ], implemented by the bioconductor package rankprod, which provided a target list of 450 genes for go analysis that are highly scored in all three comparisons. we also applied dss-single on each pair of matched cancer/normal samples using […]


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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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