PoTRA

DOI: 10.18129/B9.bioc.PoTRA    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see PoTRA.

PoTRA: Pathways of Topological Rank Analysis

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

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

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
Text		NEWS

Details

biocViews	BioCarta, DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software, StatisticalMethod
Version	1.4.0
In Bioconductor since	BioC 3.9 (R-3.6) (1.5 years)
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_1.4.0.tar.gz
Windows Binary	PoTRA_1.4.0.zip
macOS 10.13 (High Sierra)	PoTRA_1.4.0.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	https://bioconductor.org/packages/PoTRA/
Package Downloads Report	Download Stats