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:

1. Physical proximity (or linkage disequilibrium with) trait-related SNPs;
2. Presence in coexpression modules enriched in guide genes (i.e., “reference” genes that are known to be associated with the phenotype).
3. 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.