ArticleBioinformatics (Oxford, England)2017
RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 9 of them syntheses that pooled it.
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Who cites it
82 citing papers in PubMed, 9 syntheses or guidelines pooled it.
- An ancestral molecular response to nanomaterial particulates.Nature nanotechnology · 2023Pooled it
- Deciphering the sex bias in housekeeping gene expression in adipose tissue: a comprehensive meta-analysis of transcriptomic studies.Biology of sex differences · 2023Pooled it
- Pooled it
- Transcriptomics and network analysis highlight potential pathways in the pathogenesis of pterygium.Scientific reports · 2022Pooled it
- Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor.Molecular systems biology · 2021Pooled it
- Comparison of tumour and serum specific microRNA changes dissecting their role in pancreatic ductal adenocarcinoma: a meta-analysis.BMC cancer · 2019Pooled it
- SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data.Bioinformatics (Oxford, England) · 2019Pooled it
- Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1.BMC medical genomics · 2019Pooled it
- Pooled it
- Transcriptome analysis of early pregnancy vitamin D status and spontaneous preterm birth.PloS one · 2020Trial
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- AWmeta Empowers Adaptively Weighted Transcriptomic Meta-Analysis.Current issues in molecular biology · 2026Article
- TbTim20 facilitates protein import at a low membrane potential in trypanosomes lacking the mitochondrial genome.The FEBS journal · 2026Article
- MUUMI: an R package for statistical and network-based meta-analysis for multi-omics data integration.BMC bioinformatics · 2026Article
- MetaOmixTools: A User-Friendly Web Suite for Meta-analysis of Ranked Features and Functional Enrichment.Computational and structural biotechnology journal · 2026Article
- Krüppel-like factor 4 regulates cellular proliferation and differentiation in human bone marrow-derived mesenchymal stem cells.Biochemistry and biophysics reports · 2025Article
- Genetic Insight into Expression-Defined Melanoma Subtypes and Network Mechanisms: An in Silico Study.Genes · 2025Article
- A trypanosome-specific complex mediates late-stage processing of cytosolic LSU rRNA.Nucleic acids research · 2025Article
- PEX39 facilitates the peroxisomal import of PTS2-containing proteins.Nature cell biology · 2025Article
- Silencing mitochondrial gene expression in living cells.Science (New York, N.Y.) · 2025Article
22 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
motivationThe Rank Product (RP) is a statistical technique widely used to detect differentially expressed features in molecular profiling experiments such as transcriptomics, metabolomics and proteomics studies. An implementation of the RP and the closely related Rank Sum (RS) statistics has been available in the RankProd Bioconductor package for several years. However, several recent advances in the understanding of the statistical foundations of the method have made a complete refactoring of the existing package desirable.
resultsWe implemented a completely refactored version of the RankProd package, which provides a more principled implementation of the statistics for unpaired datasets. Moreover, the permutation-based P -value estimation methods have been replaced by exact methods, providing faster and more accurate results. AVAILABILITY AND IMPLEMENTATION: RankProd 2.0 is available at Bioconductor ( https://www.bioconductor.org/packages/devel/bioc/html/RankProd.html ) and as part of the mzMatch pipeline ( http://www.mzmatch.sourceforge.net ). CONTACT: rainer.breitling@manchester.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.