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

DOI: 10.18129/B9.bioc.ToPASeq

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

Need some help? Ask on the Bioconductor Support site!

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

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