PoTRA

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PoTRA.

PoTRA: Pathways of Topological Rank Analysis


Bioconductor version: 3.9

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 (!require("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")
Pathways of Topological Rank Analysis (PoTRA) HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BioCarta, DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, Pathways, Reactome, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License LGPL
Depends R (>= 3.6.0), stats, BiocGenerics, org.Hs.eg.db, igraph, graph, graphite
Imports
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Suggests BiocStyle, knitr, rmarkdown, colr, metap, repmis
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package PoTRA_1.0.0.tar.gz
Windows Binary PoTRA_1.0.0.zip
Mac OS X 10.11 (El Capitan) PoTRA_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PoTRA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PoTRA
Bioc Package Browser https://code.bioconductor.org/browse/PoTRA/
Package Short Url https://bioconductor.org/packages/PoTRA/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive