cageminer
This is the development version of cageminer; for the stable release version, see cageminer.
Candidate Gene Miner
Bioconductor version: Development (3.20)
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
Author: FabrÃcio Almeida-Silva [aut, cre] , Thiago Venancio [aut]
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("cageminer")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("cageminer")
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("cageminer")
Mining high-confidence candidate genes with cageminer | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation |
Version | 1.11.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 years) |
License | GPL-3 |
Depends | R (>= 4.1) |
Imports | ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO |
System Requirements | |
URL | https://github.com/almeidasilvaf/cageminer |
Bug Reports | https://support.bioconductor.org/t/cageminer |
See More
Suggests | testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo |
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 | cageminer_1.11.0.tar.gz |
Windows Binary | cageminer_1.11.0.zip |
macOS Binary (x86_64) | cageminer_1.11.0.tgz |
macOS Binary (arm64) | cageminer_1.11.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/cageminer |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cageminer |
Bioc Package Browser | https://code.bioconductor.org/browse/cageminer/ |
Package Short Url | https://bioconductor.org/packages/cageminer/ |
Package Downloads Report | Download Stats |