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cageminer

Candidate Gene Miner


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("cageminer")):

Installation

To install this package, start R (version "4.3") 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")
Mining high-confidence candidate genes with cageminer HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation
Version 1.8.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cageminer_1.8.0.tar.gz
Windows Binary cageminer_1.8.0.zip
macOS Binary (x86_64) cageminer_1.8.0.tgz
macOS Binary (arm64) cageminer_1.8.0.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