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>

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

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")
PhenoGeneRanker HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology
Version 1.8.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License Creative Commons Attribution 4.0 International License
Depends
Imports igraph, Matrix, foreach, doParallel, dplyr, stats, utils, parallel
System Requirements
URL
See More
Suggests knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report 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
Old Source Packages for BioC 3.17 Source Archive