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False group in <code>sc.get.aggregate</code> when obs contains NaNs

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

Status: Open.

Bug

#3903 In scverse/scanpy;

· quentinblampey opened on Nov 26, 2025

irrelevant warning in sc.readwrite.is_valid_filename

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

Status: Open.

Enhancement

#3899 In scverse/scanpy;

· nicolasrochette opened on Nov 21, 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

spaceranger’s automated cluster number detection

Needs info❔More information neededMore information needed

Status: Open.

Enhancement

#3834 In scverse/scanpy;

· asmlgkj opened on Oct 14, 2025

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