Issues

• Remove anndata pin when 0.14.0 is released

  scverse/pertpy#1071 · Filter by author Zethson opened on Aug 7, 2026
  

• Multimodal perturbation readouts (Perturb-CITE-seq, Perturb-ATAC, multiome)

  enhancement
  scverse/pertpy#1039 · Filter by author Zethson opened on Jul 7, 2026

• Spatial perturbation analysis

  enhancement
  scverse/pertpy#1038 · Filter by author Zethson opened on Jul 7, 2026

• Experimental design & power analysis for perturbation screens

  enhancement
  scverse/pertpy#1037 · Filter by author Zethson opened on Jul 7, 2026
  

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

  enhancement
  scverse/pertpy#1036 · Filter by author Zethson opened on Jul 7, 2026
  10

  

• Benchmarking & evaluation harness for perturbation prediction (baseline-aware)

  enhancement
  scverse/pertpy#1035 · Filter by author Zethson opened on Jul 7, 2026

• Response prediction: predict unseen perturbations & combinations (GEARS, CPA/chemCPA, biolord, FM embeddings)

  enhancement
  scverse/pertpy#1034 · Filter by author Zethson opened on Jul 7, 2026

• Move differential expression analysis to separate package

  enhancement
  scverse/pertpy#730 · Filter by author grst opened on Mar 19, 2025
  5

• Add linear mixed effects model to DE interface

  enhancement
  scverse/pertpy#614 · Filter by author grst opened on May 27, 2024