MarkerGenes

This repository contains gene cell-type/tissue specificity matrices, which can be used to determine the specificity of a gene to a particular cell type or tissue.

Installation instructions

To access the datasets within this package, either clone the repository to your local directory or use the following code chunk (and edit accordingly):

args <- 
  list(
    url = "https://github.com/RHReynolds/MarkerGenes/raw/master/specificity_matrices_new/ctd_aibsMultipleCrtxSmrtSeq.rda",
    file_name = "ctd_aibsMultipleCrtxSmrtSeq.rda",
    out_dir = here::here("tmp")
  )

# create temporary directory
dir.create(args$out_dir)

# check if file exists and download if it doesn't
if (!file.exists(file.path(args$out_dir, args$file_name))) {

  download.file(
    url = args$url,
    destfile = file.path(args$out_dir, args$file_name)
  )

}

To use functions within the package, install from github. This can be done using the following lines of code:

if (!requireNamespace("devtools", quietly = TRUE)) {
    install.packages("devtools")
}

devtools::install_github("RHReynolds/MarkerGenes")

Please note that there is no plan to ever submit this code to CRAN or Bioconductor. This code was developed for personal use.

Usage

For details, please refer to the vignette.

License

The code in this repository is released under an MIT license. This repository is distributed in the hope that it will be useful to the wider community, but without any warranty of any kind. Please see the LICENSE for more details.

Citation

If you use any specificity matrices from this repository, please make sure you cite the original publication the specificity values were derived from. For details, please refer to: dataset_metadata.html.

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

utils::citation("MarkerGenes")
#> 
#> Reynolds RH (2022). _MarkerGenes_.
#> https://github.com/RHReynolds/MarkerGenes - R package version 0.99.0,
#> <URL: https://github.com/RHReynolds/MarkerGenes>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {MarkerGenes},
#>     author = {Regina H. Reynolds},
#>     year = {2022},
#>     url = {https://github.com/RHReynolds/MarkerGenes},
#>     note = {https://github.com/RHReynolds/MarkerGenes - R package version 0.99.0},
#>   }

Code contents

Within this repository you will find:

Directory	Description
data	Package data.
data-raw	Scripts related to generation of data available in repository
docs	Source files for repository website
flat_lists	Marker genes from various sources, as described in folder readme.txt
inst	External data used in data-raw
man	Function documentation
metadata	Metadata related to specificity matrices/dataframes
nohup_logs	For any scripts that were run outside of an `.Rmd` (e.g. scripts from the data-raw directory), a log file was recorded and can be accessed here
R	Repository functions
results	Results relating to .Rmds in workflows
specificity_df	Folder of specificity dataframes
specificity_matrices	Folder of specificity matrices compatible with the defunct EWCE v1.3.0 available on Bioconductor v3.5
specificity_matrices_new	Folder of specificity matrices compatible with the new EWCE that is available in Bioconductor>=3.14
vignettes	Repository vignette
workflows	Miscellaneous .Rmds