PoTRA
This package is for version 3.16 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: 3.16
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, Reactome, SMPDB and PharmGKB, Panther, PathBank, etc databases from the devel graphite library.
Author: Chaoxing Li, Li Liu and Valentin Dinu
Maintainer: Margaret Linan <mlinan at asu.edu>
citation("PoTRA")):
Installation
To install this package, start R (version "4.2") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, GraphAndNetwork, KEGG, Network, Panther, PathBank, Pathways, Reactome, Software, StatisticalMethod |
| Version | 1.13.0 |
| 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 | |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, colr, metap, repmis |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PoTRA_1.13.0.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 3.16 | Source Archive |