topologyGSA specifications

Information


Unique identifier OMICS_10393
Name topologyGSA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data All gene expression
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.4.6
Stability Stable
Requirements
methods, fields, graph, Rgraphviz, gRbase(≥1.7), qpgraph
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Gabriele Sales <>

topologyGSA in publications

 (2)
PMCID: 5784953
PMID: 29370226
DOI: 10.1371/journal.pone.0191154

[…] representative methods identifying differentially expressed pathways between two groups of interest based on gene expression data with prior knowledge of pathway topologies: spia, prs, cepa, tappa, topologygsa, clipper and degraph. we performed a number of controlled experiments that investigated their sensitivity to sample and pathway size, threshold-based filtering of differentially expressed […]

PMCID: 3794382
PMID: 24133454
DOI: 10.3389/fphys.2013.00278

[…] used to address this issue while still using all gene measurements uses the individual p-values of each gene (voichiţa et al., )., among the surveyed methods, scorepage, pathologist, netgsa, topologygsa, pwea, tappa, acst, bpa, bapa-iggfd, and degraph use all genes together with their expression values as input. however, for bpa and bapa-iggfd, the fold changes are only used to label […]


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