https://github.com/kpj/geneticriskandtads
Investigate TADs/SNPs and diseases
https://github.com/kpj/geneticriskandtads
Last synced: 2 months ago
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Investigate TADs/SNPs and diseases
- Host: GitHub
- URL: https://github.com/kpj/geneticriskandtads
- Owner: kpj
- Created: 2018-03-24T00:07:10.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2021-07-05T08:33:50.000Z (almost 4 years ago)
- Last Synced: 2025-01-18T04:06:57.232Z (4 months ago)
- Language: Jupyter Notebook
- Size: 40.8 MB
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Genetic Risks and Topologically-Associating Domains
A Snakemake workflow for the investigation of disease-associated SNP enrichments in topologically-associating domains.
## Usage
Run pipeline as follows:
```bash
$ snakemake -pr -j 1 --use-conda
```
## Tests
Run tests as follows:
```bash
$ ./tests/run.sh
```
# Data sources
* Hi-C data: ftp://cooler.csail.mit.edu/coolers/hg19/
* [GWAS Catalog](https://www.ebi.ac.uk/gwas/home): `v1.0.2-associations_e100_r2021-02-10`
* [DisGeNET](https://www.disgenet.org/): `DisGeNET 2020 - v7.0`
* [HumanDiseaseOntology](https://disease-ontology.org/): `r2021-01-28`
* [Experimental Factor Ontology](https://www.ebi.ac.uk/efo/): `v3.27.0`
* [SequenceOntology](http://www.sequenceontology.org/): `v3.1`