Generalized mapping scripts for RNA-seq, Patch-seq or any gene expression data. Assumes that you have built an Allen Institute Taxonomy (AIT) object with scrattch.taxonomy.
Documentation
You can find a detail description of all scrattch.mapping functions here:
Update notes are here:
Installation
Using docker (recommended)
We have setup a docker environment 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.mapping directly from GitHub as follows:
devtools::install_github("AllenInstitute/scrattch.mapping")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
- Run Flat, Tree, and Seurat taxonomy mapping This examples shows how to use scrattch.mapping for standard taxonomy mapping.
- Mapping to HMBA Basal Ganglia AIT This tutorial shows how to map against the HMBA Human and Macaque Basal Ganglia consensus taxonomies.
Reporting issues
If you run into any issues, please let Nelson and Jeremy know or create a new issue in the ‘Issues’ tab above.