DOI: 10.18129/B9.bioc.cageminer
This is the development version of cageminer; to use it, please install the devel version of Bioconductor.
Candidate Gene Miner
Bioconductor version: Development (3.14)
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
“4.1”) and enter:
if (!requireNamespace("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 | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation |
| Version | 0.99.7 |
| In Bioconductor since | BioC 3.14 (R-4.1) |
| 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 |
| SystemRequirements | |
| Enhances | |
| URL | github.com/almeidasilvaf/cageminer |
| BugReports | 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.
Read more here: Source link