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("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 | ||
| 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 | |
| Suggests Me | |
| 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 |