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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# brainstorm
<!-- badges: start -->
[](https://codecov.io/gh/LieberInstitute/brainstorm?branch=master)
[](https://github.com/LieberInstitute/brainstorm/actions/workflows/check-bioc.yml)
<!-- badges: end -->
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](http://cran.r-project.org/). Then install `brainstorm` from [Bioconductor](http://bioconductor.org/) using the following code:
```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("brainstorm")
```
And the development version from [GitHub](https://github.com/) with:
```{r 'install_dev', eval = FALSE}
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...
```{r example, eval = requireNamespace('brainstorm')}
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__.
```{r 'citation', eval = requireNamespace('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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
## Development tools
* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/) through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://.github.io/brainstorm) 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')`.