DOI: 10.18129/B9.bioc.ToPASeq    

Package for Topology-based Pathway Analysis of RNASeq data

Bioconductor version: Release (3.6)

Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a single pathway.

Author: Ivana Ihnatova, Eva Budinska

Maintainer: Ivana Ihnatova <ihnatova at>

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PDF R Script An R Package for topology-based pathway analysis of microaray and RNA-Seq data
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biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.11.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License AGPL-3
Depends graphite(>= 1.16), gRbase, graph, locfit, Rgraphviz
Imports R.utils, methods, Biobase, parallel, edgeR, DESeq2, SummarizedExperiment, RBGL, DESeq, fields, limma, TeachingDemos, KEGGgraph, qpgraph, clipper, AnnotationDbi, doParallel
LinkingTo Rcpp
Suggests RUnit, BiocGenerics, gageData, DEGraph, plotrix,
Depends On Me
Imports Me
Suggests Me
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Source Package ToPASeq_1.11.0.tar.gz
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