cageminer
This is the development version of cageminer; for the stable release version, see cageminer.
Candidate Gene Miner
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: FabrÃcio Almeida-Silva <fabricio_almeidasilva at hotmail.com>
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 |
Details
| biocViews | FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation |
| Version | 1.13.0 |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |