Search results

Change <code>leiden</code> default <code>flavor</code> to <code>None</code> and warn about impending switch to <code>igraph</code> + warn about speed of <code>igraph</code> being **much** faster

Area – ReproducibilityExact replicationExact replication

dependenciesPull requests that update a dependency filePull requests that update a dependency file

Status: Open.

Enhancement

#3911 In scverse/scanpy;

· ilan-gold opened on Dec 11, 2025

<code>pp.regress_out</code> fails with to many CPU-Cores

Status: Open.

Bug

#3910 In scverse/scanpy;

· Intron7 opened on Dec 11, 2025

·  

1.12.0

read_10x_mtx cannot deal with numerical gene symbols

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Bug

#3909 In scverse/scanpy;

· arteymix opened on Dec 9, 2025

Document dask support for highly variable genes

Area - Documentation 📒

Area - Out of core 💾Working with on disk dataWorking with on disk data

Status: Open.

Enhancement

#3892 In scverse/scanpy;

· ivirshup opened on Nov 12, 2025

·  

1.12.0

Exposing some functions <code>squidpy</code> uses

Area – APIAPI designAPI design

Status: Open.

Enhancement

#3891 In scverse/scanpy;

· selmanozleyen opened on Nov 12, 2025

Highly Variable Genes Selection using CSC <code>dask</code>

Area - Out of core 💾Working with on disk dataWorking with on disk data

Area – Performance 🐌

Status: Open.

Enhancement

#3862 In scverse/scanpy;

· ilan-gold opened on Oct 30, 2025

·  

1.13.0

Implementation of <code>sc.tl.score_genes</code> doesn't match reference

Status: Open.

Bug

#3845 In scverse/scanpy;

· MLubetzki opened on Oct 23, 2025

Support values_to_plot in pl.rank_genes_groups_matrixplot and pl.rank_genes_groups_heatmap (parity with dotplot)

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Enhancement

#3842 In scverse/scanpy;

· asmlgkj opened on Oct 21, 2025

Regressing out variables in pearson residual normalization (SCTransform)

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Open.

Enhancement

#3838 In scverse/scanpy;

· Li-ZhiD opened on Oct 20, 2025

Improve flexibility of <code>sc.pp.scrublet()</code>

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3837 In scverse/scanpy;

· zekepuli opened on Oct 17, 2025

·  

1.13.0

Export more types

Area – APIAPI designAPI design

Status: Open.

Enhancement

#3826 In scverse/scanpy;

· flying-sheep opened on Oct 2, 2025

Apple Silicon: Accelerate or openBLAS for Numpy

Question

Status: Open.

Enhancement

#3823 In scverse/scanpy;

· mxp0wr opened on Sep 30, 2025