PoTRA

DOI: 10.18129/B9.bioc.PoTRA    

This is the development version of PoTRA; to use it, please install the devel version of Bioconductor.

PoTRA: Pathways of Topological Rank Analysis

Bioconductor version: Development (3.10)

The PoTRA analysis is based on topological ranks of genes in biological pathways. PoTRA can be used to detect pathways involved in disease (Li, Liu & Dinu, 2018). We use PageRank to measure the relative topological ranks of genes in each biological pathway, then select hub genes for each pathway, and use Fishers Exact test to determine if the number of hub genes in each pathway is altered from normal to cancer (Li, Liu & Dinu, 2018). Alternatively, if the distribution of topological ranks of gene in a pathway is altered between normal and cancer, this pathway might also be involved in cancer (Li, Liu & Dinu, 2018). Hence, we use the Kolmogorov–Smirnov test to detect pathways that have an altered distribution of topological ranks of genes between two phenotypes (Li, Liu & Dinu, 2018). PoTRA can be used with the KEGG, Biocarta, Reactome, NCI, SMPDB and PharmGKB databases from the devel graphite library.

Author: Chaoxing Li, Li Liu and Valentin Dinu

Maintainer: Valentin Dinu <valentin.dinu at asu.edu>

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

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("PoTRA")

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("PoTRA")

 

HTML R Script Pathways of Topological Rank Analysis (PoTRA)
PDF   Reference Manual

Details

biocViews BioCarta, DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software, StatisticalMethod
Version 1.1.0
In Bioconductor since BioC 3.9 (R-3.6) (< 6 months)
License LGPL
Depends R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph, graph, graphite
Imports
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, colr, metap, repmis
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 PoTRA_1.1.0.tar.gz
Windows Binary PoTRA_1.1.0.zip
Mac OS X 10.11 (El Capitan) PoTRA_1.1.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PoTRA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PoTRA
Package Short Url http://bioconductor.org/packages/PoTRA/
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: