omicverse 2.4.1

omicverse 2.4.1

on Python PyPI

Bug-fix release. PyPI: https://pypi.org/project/omicverse/2.4.1/

Fixes

• ov.pp.qc in cpu-gpu-mixed mode raised NameError: name 'backend' is not defined on an in-memory AnnData (2.4.0 regression); mixed-mode QC now matches CPU mode exactly (#1032)
• remove_ambient(method='envelope') no longer pinned at the lower clip at low contamination (cross-fitted panel); panel_gene_map maps aSMA to ACTA2; a second library of one person no longer breaks resolve_sample_relationships (#1030)
• ov.pp.scdblfinder / qc(doublets_method='scdblfinder'): expected doublet rate 1% per 1000 cells, as R scDblFinder (#1031)

Bulk

• limma from PyPI (python-limma>=0.1.1) instead of a vendored copy (#1029)

Full notes: https://github.com/omicverse/omicverse-tutorials/blob/main/docs/Release_notes.md