cageminer

DOI: 10.18129/B9.bioc.cageminer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cageminer.

Candidate Gene Miner

Bioconductor version: 3.16

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: Fabrício Almeida-Silva [aut, cre] , Thiago Venancio [aut]

Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	Mining high-confidence candidate genes with cageminer
PDF		Reference Manual
Text		NEWS

Details

biocViews	FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation
Version	1.4.0
In Bioconductor since	BioC 3.14 (R-4.1) (1.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO
LinkingTo
Suggests	testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo
SystemRequirements
Enhances
URL	https://github.com/almeidasilvaf/cageminer
BugReports	https://support.bioconductor.org/t/cageminer
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	cageminer_1.4.0.tar.gz
Windows Binary	cageminer_1.4.0.zip
macOS Binary (x86_64)	cageminer_1.4.0.tgz
macOS Binary (arm64)	cageminer_1.4.0.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