https://github.com/alleninstitute/scrattch.mapping
Genearlized mapping scripts for RNA-seq and Patch-seq data
https://github.com/alleninstitute/scrattch.mapping
Last synced: 10 months ago
JSON representation
Genearlized mapping scripts for RNA-seq and Patch-seq data
- Host: GitHub
- URL: https://github.com/alleninstitute/scrattch.mapping
- Owner: AllenInstitute
- Created: 2022-11-29T19:33:57.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-05-14T22:49:40.000Z (about 1 year ago)
- Last Synced: 2025-09-09T04:22:26.608Z (10 months ago)
- Language: R
- Size: 4.12 MB
- Stars: 15
- Watchers: 5
- Forks: 3
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# scrattch.mapping
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](https://github.com/AllenInstitute/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](https://github.com/AllenInstitute/scrattch/blob/master/README.md#using-docker) for [the parent scrattch package](https://github.com/AllenInstitute/scrattch) 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](https://r-forge.r-project.org/R/?group_id=947) if you use Windows. Vignettes are provided below.
## Usage examples
1. [**Run Flat, Tree, and Seurat taxonomy mapping**](https://github.com/AllenInstitute/scrattch-mapping/blob/main/examples/mapping.md) This examples shows how to use scrattch.mapping for standard taxonomy mapping.
2. [**Mapping to HMBA Basal Ganglia AIT**](https://github.com/AllenInstitute/scrattch-mapping/blob/main/examples/mapping_BasalGanglia.md) 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**](https://github.com/AllenInstitute/scrattch-mapping/issues).