
<!-- README.md is generated from README.Rmd. Please edit that file -->

# brainflowprobes

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This package can be used to annotate candidate target probe sequences
designed to label RNA in nuclei isolated from human postmortem brain for
flow cytometry. This package also includes functions that visualize
candidate sequence expression in four postmortem brain datasets that
address nuclear expression, effects of RNA degradation and flow
cytometric sorting, and cell type-specific expression to increase the
likelihood of success as a custom target probe. Please refer to the
BrainFlow publication or the [PrimeFlow RNA(TM) Assay
Kit](https://www.thermofisher.com/order/catalog/product/88-18005-204)
literature for more information.

## Documentation

For more information about `brainflowprobes` check the vignettes
[through Bioconductor](http://bioconductor.org/packages/brainflowprobes)
or at the [documentation
website](http://lieberinstitute.github.io/brainflowprobes).

## Installation instructions

Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `brainflowprobes` using
from [Bioconductor](http://bioconductor.org/) the following code:

``` r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("brainflowprobes")
```

## Citation

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

``` r
print(citation('brainflowprobes'), bibtex = TRUE)
#> 
#> Price AJ (2020). _Plots and annotation for choosing BrainFlow target
#> probe sequence_. doi: 10.18129/B9.bioc.brainflowprobes (URL:
#> https://doi.org/10.18129/B9.bioc.brainflowprobes),
#> https://github.com/LieberInstitute/brainflowprobes - R package version
#> 1.1.1, <URL: http://www.bioconductor.org/packages/brainflowprobes>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {Plots and annotation for choosing BrainFlow target probe sequence},
#>     author = {Amanda J Price},
#>     year = {2020},
#>     url = {http://www.bioconductor.org/packages/brainflowprobes},
#>     note = {https://github.com/LieberInstitute/brainflowprobes - R package version 1.1.1},
#>     doi = {10.18129/B9.bioc.brainflowprobes},
#>   }
```

Please note that the `brainflowprobes` 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 derfinderPlot 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 *[usethis](https://CRAN.R-project.org/package=usethis)*,
    *[remotes](https://CRAN.R-project.org/package=remotes)*,
    *[sysreqs](https://github.com/r-hub/sysreqs)* and
    *[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)*
    customized to use [Bioconductor’s docker
    containers](https://www.bioconductor.org/help/docker/) and
    *[BiocCheck](https://bioconductor.org/packages/3.11/BiocCheck)*.
  - Code coverage assessment is possible thanks to
    [codecov](https://codecov.io/gh) and
    *[covr](https://CRAN.R-project.org/package=covr)*.
  - The [documentation
    website](http://lieberinstitute.github.io/brainflowprobes) is
    automatically updated thanks to
    *[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
  - The code is styled automatically thanks to
    *[styler](https://CRAN.R-project.org/package=styler)*.
  - The documentation is formatted thanks to
    *[devtools](https://CRAN.R-project.org/package=devtools)* and
    *[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.

For more details, check the `dev` directory.
