Spatial perturbation analysis
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 345
- Forks
- 66
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 13
Description
Context
Perturbation experiments are increasingly read out in spatial context (spatial Perturb-seq, and perturbation effects on tissue neighborhoods and cell–cell communication).
pertpy is currently non-spatial; Milo tests neighborhoods on a kNN graph but does not use spatial coordinates.
To add
- Perturbation-effect testing that respects spatial neighborhoods / niches.
- Changes in cell–cell communication or niche composition as a function of perturbation.
- Interoperability with squidpy / SpatialData so spatial perturbation data flows into the perturbation-space and distance tooling.
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
The issue names no files, tests, or entry points. Start by mapping the existing perturbation-space and distance tooling, then review how interoperability with squidpy and SpatialData is handled. Done requires spatial-neighborhood perturbation testing, niche or cell–cell communication comparisons, and spatial data flowing through the relevant tooling.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100