npGSEA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool npGSEA

Tool usage distribution map

This map represents all the scientific publications referring to npGSEA per scientific context
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Associated diseases


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npGSEA specifications


Unique identifier OMICS_08550
Name npGSEA
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 1.16.0
Stability Stable
limma, methods, stats, graphics, BiocGenerics, Biobase, BiocStyle, genefilter, hgu95av2.db, ALL, GSEABase(>=1.24.0), ReportingTools
Maintained Yes


No version available



  • person_outline Jessica Larson

Publication for npGSEA


Moment based gene set tests

2015 BMC Bioinformatics
PMCID: 4419444
PMID: 25928861
DOI: 10.1186/s12859-015-0571-7

npGSEA citations


Patient derived xenografts undergo murine specific tumor evolution

Nat Genet
PMCID: 5659952
PMID: 28991255
DOI: 10.1038/ng.3967

[…] inter-lineage differences by including lineage as a covariate in the model. Gene set testing was performed using a parametric approximation to permutation-based testing, implemented in the R package npGSEA. Inter-lineage differences were controlled for by regressing lineage out of both the arm-level CNA calls and the variable of interest. […]


Overlapping Group Logistic Regression with Applications to Genetic Pathway Selection

Cancer Inform
PMCID: 5026200
PMID: 27679461
DOI: 10.4137/CIN.S40043

[…] pproaches and regression models with respect to their implications for pathway selection. Thus, although a variety of extensions and refinements of GSEA have been proposed, such as GSEAlm, ROAST, and npGSEA, we restrict our attention here to GSEA, the most well-known and widely used method in this group.Finally, we provide a publicly available implementation of the OGLasso method described in this […]

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npGSEA institution(s)
Department of Bioinformatics and Computational Biology, Genentech, Inc, South San Francisco, USA

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