ToPASeq

DOI: 10.18129/B9.bioc.ToPASeq    

Topology-based pathway analysis of RNA-seq data

Bioconductor version: Release (3.7)

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: Ludwig Geistlinger <ludwig.geistlinger at sph.cuny.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ToPASeq")

Documentation

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

Details

biocViews DifferentialExpression, GeneExpression, GraphAndNetwork, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version 1.14.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License AGPL-3
Depends R (>= 3.5.0), graphite
Imports Rcpp, graph, methods
LinkingTo Rcpp
Suggests BiocStyle, EnrichmentBrowser, airway, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package ToPASeq_1.14.0.tar.gz
Windows Binary ToPASeq_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) ToPASeq_1.14.0.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 http://bioconductor.org/packages/ToPASeq/
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