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seq2pathway is a tool for the functional gene-set analysis of genomic loci in RNA-seq data sets. The seq2pathway algorithm assigns genes to the pathways and computes gene-level pathway scores.


ChIP-seq; RNA-Seq; GWAS study


  • Operation: Pathway or network analysis; RNA-Seq analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.18.0
  • Maturity: Stable
  • Credit: The National Institutes of Health.
  • Contact: Xinan Yang xyang2 _at_ with contribution from Zhezhen Wang zhezhen _at_
  • Collection: Bioconductor


Wang B, Cunningham JM, Yang XH "Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data." Bioinformatics. 2015 Sep 15;31(18):3043-5. Epub 2015 May 15.
PMID: 25979472
PMCID: PMC4565027

Yang X, Regan K, Huang Y, Zhang Q, Li J, Seiwert TY, Cohen EE, Xing HR, Lussier YA "Single sample expression-anchored mechanisms predict survival in head and neck cancer." PLoS Comput. Biol. 2012; 8(1):e1002350
PMID: 22291585
PMCID: PMC3266878

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21.
PMID: 25633503
PMCID: PMC4509590

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15.
PMID: 15461798
PMCID: PMC545600

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