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scrattch.taxonomy

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.

Documentation

You can find a detail description of scrattch.taxonomy (OUTDATED – FIX) functions here:

Update notes are here: Versions

Installation

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.

Directly from GitHub (strongly discouraged)

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.

Usage examples

  1. 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.
  2. Check a Shiny taxonomy and convert to AIT This example shows how you can use checkTaxonomy to see what does not abide by the AIT schema, and then use the resulting information to convert to AIT format. (Note that this example will only work for Allen Institute employees as it points to a private file.)
  3. Create a human MTG taxonomy in AIT format with a neuron only ‘child’ taxonomy This example provides a step-by-step process for downloading human MTG data from adult neurotypical humans along with the associated SEA-AD taxonomy (from here), converting it to an AIT file that aligns with the AIT schema, and adding a child taxonomy subsetting to only neuronal types for use with Patch-seq mapping (see scrattch.patchseq library).

Reporting issues

If you run into any issues, please let Nelson and Jeremy know or create a new issue in the ‘Issues’ tab above.

TODO

  • Update documentation.

Done