SnapATAC2 notebooks to reproduce CATlas results
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- Dominant language
- Python
- Stars
- 323
- Forks
- 43
- PR merge metrics
- No merged PRs in 30d
Description
I was wondering if there is any notebooks using SnapATAC2 to generate matrices provided on the catlas.org website such as the cell type x CRE matrix or cell type specific peaks.
According to the paper I believe Taiji was the framework used for the analysis but a notebook generating these matrices using the latest SnapATAC2 would be an amazing resource for the community.
Sorry if this already exists but just wanted to ask.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the CATlas cell type x CRE and cell type-specific peaks links, the Taiji reference, and any existing SnapATAC2 notebooks. Determine whether the current repository already contains relevant notebook entry points. Done means reproducible notebooks using the latest SnapATAC2 generate the referenced matrices.
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Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100