ToPASeq

DOI: 10.18129/B9.bioc.ToPASeq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ToPASeq.

Topology-based pathway analysis of RNA-seq data

Bioconductor version: 3.9

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>

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	1.18.1
In Bioconductor since	BioC 3.0 (R-3.1) (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_1.18.1.tar.gz
Windows Binary	ToPASeq_1.18.1.zip
Mac OS X 10.11 (El Capitan)	ToPASeq_1.18.1.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