GSAASeqSP statistics

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GSAASeqSP specifications


Unique identifier OMICS_05582
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for GSAASeqSP

GSAASeqSP in publications

PMCID: 5944832
PMID: 29038090
DOI: 10.1289/EHP1937

[…] mice relative to control mice, as determined by deseq2., significant enrichment of biological pathways associated with mrna and chromatin accessibility differences was determined using gsaaseqsp v. 1.2 ( (; ) and the reactome pathway database (; ; ). the number of permutations was set to 2,000. pathways with fewer than 15 genes or more than 500 genes […]

PMCID: 5491171
PMID: 28662214
DOI: 10.1371/journal.pone.0180258

[…] modulation of the immune system and various aspects of cell metabolism., to complement our fidea and kegg pathway analysis, we used the gene set association analysis with sequence permutation (gsaaseqsp) program, which is specific for rna-seq data [], with the broad institute’s molecular signatures hallmark database (msigdb), which groups genes based on known functions []. as shown in , […]

PMCID: 5222877
PMID: 28119706
DOI: 10.3389/fpls.2016.02007

[…] analysis for three pairs of samples, 4-2, 6-2, and 8-2 wap, to identify pathways/gene sets significantly changed during seed development. gene set association analysis was carried out using gsaaseqsp 2.0 (). rna-seq raw counts were normalized by the deseq normalization (). we chose signal2 noise for gene-level differential expression analysis and weighted_ks for gene set association […]

PMCID: 5249248
PMID: 28056084
DOI: 10.1371/journal.pgen.1006552

[…] gene set association analysis for polysomal and total fractions was performed by gsaa software (version 1.2) []. raw reads for about ~ 22000 genes identified by entrez gene id were analyzed by gsaaseqsp, using gene set c5 (mouse version retrieved from and specifying as permutation type ‘gene set’ and as gene set size filtering min 15 and max 800., […]

PMCID: 5133678
PMID: 27957556
DOI: 10.1016/j.heliyon.2016.e00204

[…] development and progression (; )., to complement our kegg pathway results, we used an additional pathway analysis program − the gene set association analysis for rna-seq with sample permutation (gsaaseqsp) program () - as it takes into account inherent bias present in rna-seq data. in combination with the broad institute’s molecular signatures database (msigdb) hallmark gene set (), genes […]

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GSAASeqSP institution(s)
Department of Computer Science and Technology, Department of Statistics, Southwest University, Chongqing, China; Department of Statistical Science, Department of Computer Science, and Department of Mathematics, Duke University, Durham, NC, USA; Department of Genetics, Department of Biology, Lineberger Comprehensive Cancer Center, and Carolina Center for Genomics and Society, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
GSAASeqSP funding source(s)
This work was supported by Key Discipline Fund of National 211 Project (SWU:TR201208-3), The Open Fund of State Key Laboratory of Silkworm Genome Biology (sklsgb2013005), NIH grant 1RC1CA146849, University Cancer Research Fund at UNC-CH, CA123175-01A1, NIH Systems Biology Center Grant, NSF grant DMS-0732260, NSF grant CCF-1049290, and R01 CA125618-01.

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