https://github.com/satijalab/azimuth-references
https://github.com/satijalab/azimuth-references
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/satijalab/azimuth-references
- Owner: satijalab
- Created: 2021-01-10T03:47:33.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-11-05T20:45:18.000Z (7 months ago)
- Last Synced: 2025-04-07T19:04:17.853Z (about 2 months ago)
- Language: R
- Size: 10.8 MB
- Stars: 22
- Watchers: 3
- Forks: 11
- Open Issues: 13
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Metadata Files:
- Readme: README.md
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README
# azimuth-references
Repo with workflows for generating azimuth reference objects.
# Overview
This repository contains the Dockerfile and snakemake workflows that are used to generate the azimuth references that are hosted online. Each reference directory contains a `Snakefile` and associated scripts that can be run to regenerate each reference (and associated demo data) from publicly available download links of the underlying data. To run:
```
snakemake --use-singularity --cores 1 all
```
# Reference format
The Azimuth package provides the `AzimuthReference` function to facilitate converting existing Seurat objects into the specific format expected by Azimuth. Details on the required reference format can be viewed [here](https://github.com/satijalab/azimuth/wiki/Azimuth-Reference-Format). For examples starting with a Seurat object, see the `export.R` scripts in the workflows in this repo (e.g. [human pancreas](https://github.com/satijalab/azimuth-references/blob/master/human_pancreas/scripts/export.R)).