scverse / scverse/pertpy

Drug-discovery analyses: connectivity-map / signature reversal, synergy & dose-response, genetic interactions

Open
#1,036 10 comments 0 reactions 2 assignees View on GitHub

@daveringelberg is already working on this.

Since Aug 10, 2026.

enhancement
Dominant language
Python
Stars
345
Forks
66
Avg merge
1d 4h
Merged PRs (30d)
13

Description

Context

pertpy already ships the drug/MoA/compound metadata scaffolding (pt.md.Drug, pt.md.Moa, pt.md.Compound) and drug2cell Enrichment, but not the analyses that consume it.
These are core pharma workflows sitting right next to metadata we already provide.

What's missing

  • Connectivity-map / signature reversal (LINCS/L1000-style): given a disease/query signature, rank perturbations by how strongly they reverse it. Complements drug2cell enrichment.
  • Synergy models for combinations: Bliss / Loewe combination-index models. Cinemaot covers single-cell synergy via optimal transport, but not the classic combination-index framework.
  • Dose-response curve fitting: Hill / EC50 / IC50 as first-class output, building on the dose-response quantification already in the perturbation-space base class.
  • Genetic-interaction / epistasis scoring (Norman 2019-style GI scores) for double perturbations.

Proposal / API

Add these under pertpy.tools, reusing the perturbation-space representations and Distance metrics where possible.
Signature reversal can operate on perturbation-space embeddings; GI scoring on paired-vs-single perturbation representations.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.