ToPASeq

DOI: 10.18129/B9.bioc.ToPASeq    

This package is for version 3.10 of Bioconductor; for the 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 (!requireNamespace("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")

 

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

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, ImmunoOncology, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.20.0
In Bioconductor since BioC 3.0 (R-3.1) (5.5 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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
Package Short Url https://bioconductor.org/packages/ToPASeq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: