cageminer

This is the development version of cageminer; for the stable release version, see cageminer.

Candidate Gene Miner

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-5314-2964 , Thiago Venancio [aut] ORCID: 0000-0002-2215-8082

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

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

Installation

To install this package, start R (version "4.5") 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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation
Version	1.15.2
In Bioconductor since	BioC 3.14 (R-4.1) (4 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

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_1.15.2.tar.gz
Windows Binary (x86_64)	cageminer_1.15.0.zip
macOS Binary (x86_64)	cageminer_1.15.2.tgz
macOS Binary (arm64)	cageminer_1.15.2.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