Interest in HTO/ADT demultiplexing and analysis?
Open
Nobody has claimed this yet.
Area – External
- Dominant language
- Python
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- Merged PRs (30d)
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Description
I'm starting to regularly analyze samples multiplexed with HTOs a la Stoeckius et al and multimodal CITE-seq ADTs. I have some rough ports of Seurat's HTODemux and some other functionality.
Is anyone else analyzing these kinds of experiments using scanpy and is there interest to bring functionality to do so into the main scanpy branch?
Contributor guide
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 issue's linked Stoeckius et al. paper, the rough ports of Seurat's HTODemux mentioned in the issue, and how related functionality could fit into Scanpy. Done would require an agreed scope and accepted implementation for HTO and ADT demultiplexing and analysis in the main Scanpy branch.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100