Generalized taxonomy building scripts for RNA-seq based taxonomies following the Allen Institute schema.
A list of available taxonomies in this format is available at Taxonomy_list.md. As of 10 November 2023, these represent published single-cell RNAseq taxonomies from the Allen Institute and other groups, and are largely complementary to taxonomies included at the Brain Knowledge Platform, although efforts to integrate are ongoing.
You can find a detail description of all scrattch.taxonomy functions here:
Update notes are here:
We have setup a docker environemnt for scrattch.taxonomy, scrattch.mapping, and scrattch.patchseq that contains all the required dependencies and the current version of all scrattch packages. See the readme for the parent scrattch package for the most up-to-date docker information.
While we advise using the provided docker, you can also install scrattch.taxonomy directly from GitHub as follows:
devtools::install_github("AllenInstitute/scrattch.taxonomy")
This strategy might not work due to complicated dependencies. Also note that doMC may need to be installed manually from HERE if you use Windows. Vignettes are provided below.
- Build a Shiny taxonomy This example provides the basics for creating a new taxonomy compatible with scrattch.mapping mapping functions and (internal Allen Institute) MolGen Shiny tools.
If you run into any issues, please let Nelson and Jeremy know or create a new issue in the 'Issues' tab above.
- Update documentation.