PhenoGeneRanker

DOI: 10.18129/B9.bioc.PhenoGeneRanker    

This is the development version of PhenoGeneRanker; for the stable release version, see PhenoGeneRanker.

PhenoGeneRanker: A gene and phenotype prioritization tool

Bioconductor version: Development (3.15)

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 "4.2") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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Details

biocViews BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (0.5 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_1.3.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) PhenoGeneRanker_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/PhenoGeneRanker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PhenoGeneRanker
Package Short Url https://bioconductor.org/packages/PhenoGeneRanker/
Package Downloads Report Download Stats

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