Name Mode Size
.github 040000
R 040000
data 040000
dev 040000
inst 040000
man 040000
tests 040000
vignettes 040000
.Rbuildignore 100644 0 kb
.gitignore 100644 0 kb
DESCRIPTION 100644 2 kb
NAMESPACE 100644 1 kb 100644 0 kb
README.Rmd 100644 4 kb 100644 4 kb
codecov.yml 100644 0 kb
<!-- is generated from README.Rmd. Please edit that file --> # cageminer <img src='man/figures/logo.png' align="right" height="139" /> <!-- badges: start --> [![GitHub issues](]( [![Lifecycle: stable](]( [![R-CMD-check-bioc](]( [![Codecov test coverage](]( <!-- badges: end --> 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: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) { install.packages("BiocManager") } BiocManager::install("cageminer") ``` And the development version from [GitHub]( with: ``` r 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**. ``` r 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. #> #> #> 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 = {}, #> 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](*.