PhenoGeneRanker

PhenoGeneRanker: A gene and phenotype prioritization tool


Bioconductor version: Release (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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")
PhenoGeneRanker HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology
Version 1.12.0
In Bioconductor since BioC 3.13 (R-4.1) (3.5 years)
License Creative Commons Attribution 4.0 International License
Depends
Imports igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel
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Suggests knitr, rmarkdown
Linking To
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Depends On Me
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Package Archives

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

Source Package PhenoGeneRanker_1.12.0.tar.gz
Windows Binary (x86_64) PhenoGeneRanker_1.12.0.zip
macOS Binary (x86_64) PhenoGeneRanker_1.12.0.tgz
macOS Binary (arm64) PhenoGeneRanker_1.12.0.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