brainflowprobes

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 literature for more information.

Documentation

For more information about brainflowprobes check the vignettes through Bioconductor or at the documentation website.

Installation instructions

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

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.

print(citation("brainflowprobes"), bibtex = TRUE)
#> To cite package 'brainflowprobes' in publications use:
#> 
#>   Price AJ (2023). _Plots and annotation for choosing BrainFlow target
#>   probe sequence_. doi:10.18129/B9.bioc.brainflowprobes
#>   <https://doi.org/10.18129/B9.bioc.brainflowprobes>,
#>   https://github.com/LieberInstitute/brainflowprobes - R package
#>   version 1.15.0,
#>   <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 = {2023},
#>     url = {http://www.bioconductor.org/packages/brainflowprobes},
#>     note = {https://github.com/LieberInstitute/brainflowprobes - R package version 1.15.0},
#>     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. 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, sysreqs 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.