PhenoGeneRanker

DOI: 10.18129/B9.bioc.PhenoGeneRanker  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see PhenoGeneRanker.

PhenoGeneRanker: A gene and phenotype prioritization tool

Bioconductor version: 3.17

This package is a gene/phenotype prioritization tool that utilizes multiplex heterogeneous gene phenotype network. PhenoGeneRanker allows multi-layer gene and phenotype networks. It also calculates empirical p-values of gene/phenotype ranking using random stratified sampling of genes/phenotypes based on their connectivity degree in the network. https://dl.acm.org/doi/10.1145/3307339.3342155.

Author: Cagatay Dursun [aut, cre]

Maintainer: Cagatay Dursun <cagataydursun at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("PhenoGeneRanker")

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("PhenoGeneRanker")

 

HTML	R Script	PhenoGeneRanker
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology
Version	1.8.0
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	Creative Commons Attribution 4.0 International License
Depends
Imports	igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel
LinkingTo
Suggests	knitr, rmarkdown
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	PhenoGeneRanker_1.8.0.tar.gz
Windows Binary	PhenoGeneRanker_1.8.0.zip (64-bit only)
macOS Binary (x86_64)	PhenoGeneRanker_1.8.0.tgz
macOS Binary (arm64)	PhenoGeneRanker_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/PhenoGeneRanker
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/PhenoGeneRanker
Bioc Package Browser	https://code.bioconductor.org/browse/PhenoGeneRanker/
Package Short Url	https://bioconductor.org/packages/PhenoGeneRanker/
Package Downloads Report	Download Stats