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Follow scanpy's move to igraph as the default leiden flavor

Status: Open.

#1217 In openpipelines-bio/openpipeline;

· jakubmajercik opened on Jul 16, 2026

Rename --intersect_obs parameter

Status: Open.

#1194 In openpipelines-bio/openpipeline;

· dorien-er opened on Jun 1, 2026

Bump scvelo to v0.3.4

Status: Open.

#1179 In openpipelines-bio/openpipeline;

· DriesSchaumont opened on Apr 27, 2026

Add BEYOND workflows

Status: Open.

#1161 In openpipelines-bio/openpipeline;

· mdgrv opened on Apr 10, 2026

Details are not stored by highly_variable_features_scanpy when flavor="seurat_v3"

Status: Open.

#1143 In openpipelines-bio/openpipeline;

· lazappi opened on Mar 3, 2026

highly_variable_features_scanpy does not store flavor

Status: Open.

#1141 In openpipelines-bio/openpipeline;

· lazappi opened on Feb 25, 2026

Mitochondrial/ribosomal genes are not detected in QC workflow tests

Status: Open.

#1135 In openpipelines-bio/openpipeline;

· lazappi opened on Feb 5, 2026

Move components to separate packages

Status: Open.

#1029 In openpipelines-bio/openpipeline;

· rcannood opened on May 19, 2025

Ingestion changes

enhancementNew feature or requestNew feature or request

Status: Open.

#965 In openpipelines-bio/openpipeline;

· rcannood opened on Feb 6, 2025

Create mudata namespace an move components that perform basic operation on the mudata objec to it (delete_layer, remove_modality). Most of these currently are put in the metadata or filter namespace.

Status: Open.

#770 In openpipelines-bio/openpipeline;

· DriesSchaumont opened on Mar 26, 2024

TODO list for the paper

Status: Open.

#738 In openpipelines-bio/openpipeline;

· VladimirShitov opened on Mar 8, 2024

Update scarches component

Status: Open.

#709 In openpipelines-bio/openpipeline;

· VladimirShitov opened on Feb 15, 2024