In LieberInstitute/brainstorm_package: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)

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)

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 r BiocStyle::CRANpkg('usethis'), r BiocStyle::CRANpkg('remotes'), and r BiocStyle::CRANpkg('rcmdcheck') customized to use Bioconductor's docker containers and r BiocStyle::Biocpkg('BiocCheck').
• Code coverage assessment is possible thanks to codecov and r BiocStyle::CRANpkg('covr').
• The documentation website is automatically updated thanks to r BiocStyle::CRANpkg('pkgdown').
• The code is styled automatically thanks to r BiocStyle::CRANpkg('styler').
• The documentation is formatted thanks to r BiocStyle::CRANpkg('devtools') and r BiocStyle::CRANpkg('roxygen2').

For more details, check the dev directory.

This package was developed using r BiocStyle::Biocpkg('biocthis').

LieberInstitute/brainstorm_package documentation built on Dec. 14, 2024, 10:29 p.m.