ToPASeq

DOI: 10.18129/B9.bioc.ToPASeq    

Package for Topology-based Pathway Analysis of RNASeq data

Bioconductor version: Release (3.6)

Implementation of seven methods for topology-based pathway analysis of both RNASeq and microarray data: SPIA, DEGraph, TopologyGSA, TAPPA, PRS, PWEA and a visualization tool for a single pathway.

Author: Ivana Ihnatova, Eva Budinska

Maintainer: Ivana Ihnatova <ihnatova at iba.muni.cz>

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

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

browseVignettes("ToPASeq")

 

PDF	R Script	An R Package for topology-based pathway analysis of microaray and RNA-Seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, NetworkEnrichment, Pathways, RNASeq, Software, Visualization
Version	1.11.0
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 years)
License	AGPL-3
Depends	graphite(>= 1.16), gRbase, graph, locfit, Rgraphviz
Imports	R.utils, methods, Biobase, parallel, edgeR, DESeq2, SummarizedExperiment, RBGL, DESeq, fields, limma, TeachingDemos, KEGGgraph, qpgraph, clipper, AnnotationDbi, doParallel
LinkingTo	Rcpp
Suggests	RUnit, BiocGenerics, gageData, DEGraph, plotrix, org.Hs.eg.db
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_1.11.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/ToPASeq
Package Short Url	http://bioconductor.org/packages/ToPASeq/
Package Downloads Report	Download Stats