ToPASeq

This package is for version 3.10 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: 3.10

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 iba.muni.cz>

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

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ToPASeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ToPASeq")
Eight methods for topology-based pathway analysis of RNA-seq data HTML R Script
Topology-based pathway analysis of RNA-seq data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License AGPL-3
Depends R (>= 3.5.0), graphite
Imports Rcpp, graph, methods, Biobase, RBGL, SummarizedExperiment, gRbase, limma, corpcor
System Requirements
URL
See More
Suggests BiocStyle, airway, knitr, rmarkdown, DESeq2, DESeq, edgeR, plotrix, breastCancerVDX, EnrichmentBrowser
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ToPASeq_1.20.0.tar.gz
Windows Binary ToPASeq_1.20.0.zip
Mac OS X 10.11 (El Capitan) ToPASeq_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ToPASeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ToPASeq
Bioc Package Browser https://code.bioconductor.org/browse/ToPASeq/
Package Short Url https://bioconductor.org/packages/ToPASeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive