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.
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;
Milotests neighborhoods on a kNN graph but does not use spatial coordinates.To add