PhenoGeneRanker
This is the released version of PhenoGeneRanker; for the devel version, see PhenoGeneRanker.
PhenoGeneRanker: A gene and phenotype prioritization tool
Bioconductor version: Release (3.23)
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("PhenoGeneRanker")):Cagatay Dursun. PhenoGeneRanker: PhenoGeneRanker: A gene and phenotype prioritization tool. doi:10.18129/B9.bioc.PhenoGeneRanker, R package version 1.20.0, https://bioconductor.org/packages/PhenoGeneRanker.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5.5 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PhenoGeneRanker_1.20.0.tar.gz |
| Windows Binary (x86_64) | PhenoGeneRanker_1.20.0.zip |
| macOS Binary (big-sur-x86_64) | PhenoGeneRanker_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | PhenoGeneRanker_1.20.0.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 |