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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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")| PhenoGeneRanker | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GenePrediction, GraphAndNetwork, Network, NetworkInference, Pathways, Software, SystemsBiology |
| Version | 1.21.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PhenoGeneRanker_1.21.0.tar.gz |
| Windows Binary (x86_64) | PhenoGeneRanker_1.21.0.zip |
| macOS Binary (big-sur-x86_64) | PhenoGeneRanker_1.21.0.tgz |
| macOS Binary (sonoma-arm64) | PhenoGeneRanker_1.21.0.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 |