DOI: 10.18129/B9.bioc.ToPASeq    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see ToPASeq.

Topology-based pathway analysis of RNA-seq data

Bioconductor version: 3.13

Implementation of methods for topology-based pathway analysis of RNA-seq data. This includes Topological Analysis of Pathway Phenotype Association (TAPPA; Gao and Wang, 2007), PathWay Enrichment Analysis (PWEA; Hung et al., 2010), and the Pathway Regulation Score (PRS; Ibrahim et al., 2012).

Author: Ivana Ihnatova, Eva Budinska, Ludwig Geistlinger

Maintainer: Ivana Ihnatova <ihnatova at>

Citation (from within R, enter citation("ToPASeq")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


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biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.26.0
In Bioconductor since BioC 3.0 (R-3.1) (7 years)
License AGPL-3
Depends R (>= 3.5.0), graphite
Imports Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor
LinkingTo Rcpp
Suggests BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser
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