To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

ToPASeq

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ToPASeq.

Package for Topology-based Pathway Analysis of RNASeq data

Bioconductor version: 3.1

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

Author: Ivana Ihnatova, Eva Budinska

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

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

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 1.2.0
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License AGPL-3
Depends graphite, gRbase, graph, locfit, Rgraphviz
Imports R.utils, methods, Biobase, parallel, edgeR, DESeq2, GenomicRanges, RBGL, DESeq, fields, limma, TeachingDemos, KEGGgraph, qpgraph, clipper
LinkingTo Rcpp
Suggests RUnit, BiocGenerics, gageData, DEGraph, plotrix
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.

Package Source ToPASeq_1.2.0.tar.gz
Windows Binary ToPASeq_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) ToPASeq_1.2.0.tgz
Mac OS X 10.9 (Mavericks) ToPASeq_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/ToPASeq/tree/release-3.1
Package Short Url http://bioconductor.org/packages/ToPASeq/
Package Downloads Report Download Stats

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