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ToPASeq

ToPASeq

ToPASeq is an interface tool for the pathway analysis of RNA-seq and microarray data sets. The ToPASeq can run the following tools: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA. ToPASeq also has functions for visualization, importing, and manipulation of pathways.

Topic

Transcriptomics; RNA-Seq; Molecular interactions, pathways and networks

Details

  • Operation: Pathway or network analysis
  • Software interface: Command-line user interface; Library
  • Language: R
  • Operating system: Linux; Mac OS X; Microsoft Windows
  • License: GNU AGPL v3
  • Cost: Free
  • Version name: 1.20.0
  • Maturity: Stable
  • Credit: Proteomics Core Facility of CEITEC - Central European Institute of Technology, European Regional Development Fund, RECETOX research infrastructure, Czech Ministry of Education.
  • Contact: Ivana Ihnatova ihnatova _at_ iba.muni.cz
  • Collection: Bioconductor

Publications

Ihnatova I, Budinska E "ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data." BMC Bioinformatics 2015 https://doi.org/10.1186/s12859-015-0763-1
PMID: 26514335
PMCID: PMC4625615


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. https://doi.org/10.1038/nmeth.3252
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. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600


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