cageminer

The goal of cageminer is to integrate SNP data from GWAS results with gene coexpression networks to identify high-confidence candidate genes involved in a particular phenotype. To identify high-confidence candidate genes, cageminer considers 3 criteria:

Physical proximity (or linkage disequilibrium with) trait-related SNPs;
Presence in coexpression modules enriched in guide genes (i.e., “reference” genes that are known to be associated with the phenotype).
Significant altered expression levels in a condition of interest (e.g., stress, disease, etc).

By default, cageminer defines genes as high-confidence candidates if they satisfy all of the 3 criteria above, but users can choose to use only one/some of them.

Installation instructions

Get the latest stable R release from CRAN. Then install cageminer from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("cageminer")

And the development version from GitHub with:

BiocManager::install("almeidasilvaf/cageminer")

Citation

Below is the citation output from using citation('cageminer') in R. Please run this yourself to check for any updates on how to cite cageminer.

print(citation('cageminer'), bibtex = TRUE)
#> 
#> To cite cageminer in publications use:
#> 
#>   Almeida-Silva, F., & Venancio, T. M. (2022). cageminer: an
#>   R/Bioconductor package to prioritize candidate genes by integrating
#>   genome-wide association studies and gene coexpression networks. in
#>   silico Plants, 4(2), diac018.
#>   https://doi.org/10.1093/insilicoplants/diac018
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {cageminer: an R/Bioconductor package to prioritize candidate genes by integrating genome-wide association studies and gene coexpression networks},
#>     author = {Fabricio Almeida-Silva and Thiago M. Venancio},
#>     journal = {in silico Plants},
#>     year = {2022},
#>     volume = {4},
#>     number = {2},
#>     pages = {diac018},
#>     url = {https://doi.org/10.1093/insilicoplants/diac018},
#>     doi = {10.1093/insilicoplants/diac018},
#>   }

Code of Conduct

Please note that the cageminer project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.