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npGSEA specifications

Information


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
Requirements
limma, methods, stats, graphics, BiocGenerics, Biobase, BiocStyle, genefilter, hgu95av2.db, ALL, GSEABase(>=1.24.0), ReportingTools
Maintained Yes

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Documentation


Maintainer


  • person_outline Jessica Larson <>

Publication for npGSEA

library_books

Moment based gene set tests.

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

npGSEA in publications

 (2)
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., the allelic fraction (af) and predicted effects of point […]

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

[…] 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 […]

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

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