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

Data Prep

Step 2. Correlate the Data and Identify Groups

Correlation & Grouping

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

For more details, check the dev directory.

This package was developed using biocthis.