stageR specifications


Unique identifier OMICS_16285
Name stageR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.99.02
Stability Stable
Maintained Yes




No version available



  • person_outline Lieven Clement
  • person_outline Koen Van den Berge

Publication for stageR

stageR citations


Gene level differential analysis at transcript level resolution

Genome Biol
PMCID: 5896116
PMID: 29650040
DOI: 10.1186/s13059-018-1419-z

[…] has focused on higher-order differential analysis, the complementary problem of differential analysis of individual transcripts can also benefit from some of the aggregation ideas described here. The stageR method, recently described in Van den Berge et al. [], incorporates a two-step testing procedure in which an initial meta-analysis at the gene-level (using DEXSeq) is used to identify different […]


Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids

Front Neurosci
PMCID: 5855355
PMID: 29593484
DOI: 10.3389/fnins.2018.00136

[…] do not differ between species (involving differences between species × brain part interaction terms). Hypothesis tests were assessed using a stage-wise testing procedure implemented in the R package stageR to allow for gene-level false discovery rate (FDR) control when assessing multiple research hypotheses for each gene (Van den Berge et al., ). In the screening stage, the global null hypothesis […]

stageR institution(s)
Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Krijgslaan Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium; Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
stageR funding source(s)
Supported in part by IAP research network “StUDyS” grant no. P7/06 of the Belgian government (Belgian Science Policy), the Multidisciplinary Research Partnership “Bioinformatics: from nucleotides tonetworks” of Ghent University, a Strategic Basic Research PhD grant from the Research Foundation - Flanders (FWO) and the Forschungskredit of the University of Zurich, grant no. FK-16-107.

stageR reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review stageR