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 all scrattch.taxonomy functions here:

Update notes are here:

Docker

We have setup a docker environemnt for scrattch.taxonomy and scrattch.mapping that contains all the required dependencies and the current version of both scrattch.taxonomy and scrattch.mapping. This docker is accessible through docker hub via: njjai/scrattch_mapping:0.52.2.

HPC usage:

Non-interactive

singularity exec --cleanenv docker://njjai/scrattch_mapping:0.52.2 Rscript YOUR_CODE.R

Interactive

singularity shell --cleanenv docker://njjai/scrattch_mapping:0.52.2

Installation

While we advise using the provided docker, you can also install scrattch.taxonomy directly from GitHub as follows:

# Quickly, but without the vignettes:
devtools::install_github("AllenInstitute/scrattch.taxonomy")

# More slowly, but with the vignettes:
devtools::install_github("AllenInstitute/scrattch.taxonomy", build_vignettes=TRUE, force=TRUE)

This strategy might not work outside the docker due to complicated dependencies. Also note that doMC may need to be installed manually from the download link at https://r-forge.r-project.org/R/?group_id=947 if you use Windows. Vignettes are provided below.

Usage examples

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.
Build and map against a small mouse PatchSeq taxonomy This example provides the basics for updating a taxonomy to be compatible with patchseq style mapping and visualization on (internal Allen Institute) MolGen Shiny tools.
Build and map against a human MTG PatchSeq taxonomy This example provides shows how to create a standard taxonomy and update it to be compatible with patchseq style mapping and visualization on (internal Allen Institute) MolGen Shiny tools. This example essentially combines examples 1 and 2 and applies them to human neocortical data sets. Data is from Hodge et al. (2019) for human MTG and patch-seq examples are from Berg et al (2021) (layer 2-3, excitatory neurons).

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.

AllenInstitute/scrattch.taxonomy