README.md

In joshstolz/brainstorm: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

brainstorm

The goal of brainstorm is to match genotype and RNA-seq data to conform IDs of brain samples.

Installation instructions

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

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

BiocManager::install("brainstorm")

And the development version from GitHub with:

BiocManager::install("joshstolz/brainstorm")

Workflow

Step 1. Prepare the snp Data

Step 2. Correlate the Data and Identify Groups

Step 3. Identify and Resolve Swaps

Coming Soon…

Example

TBD…

library("brainstorm")
## basic example code

Citation

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

print(citation("brainstorm"), bibtex = TRUE)
#> 
#> Stolz JM, Huuki LA, Collado-Torres L (2021). "Validating Sample Identiy
#> Through RNA-seq and DNA Genotyping Correlation." _bioRxiv_. doi:
#> 10.1101/TODO (URL: https://doi.org/10.1101/TODO), <URL:
#> https://www.biorxiv.org/content/10.1101/TODO>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation},
#>     author = {Joshua M. Stolz and Louise A. Huuki and Leonardo Collado-Torres},
#>     year = {2021},
#>     journal = {bioRxiv},
#>     doi = {10.1101/TODO},
#>     url = {https://www.biorxiv.org/content/10.1101/TODO},
#>   }

Please note that the brainstorm was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the brainstorm 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.

joshstolz/brainstorm documentation built on Aug. 10, 2021, 1:23 p.m.