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>

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 1.11.0
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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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