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Call <code>numba.set_num_threads</code> when <code>n_jobs</code> is specified (e.g. in <code>scanpy.tl.rank_genes_group</code>)

Area – Differential ExpressionDifferential expressionDifferential expression

Area – Performance 🐌

Status: Open.

Enhancement

#2390 In scverse/scanpy;

· evanbiederstedt opened on Dec 29, 2022

Add Seurat compatibility preset

Area – APIAPI designAPI design

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#3609 In scverse/scanpy;

· flying-sheep opened on Apr 24, 2025

(feat): presets

Status: Draft (not ready).

scverse/scanpynumber 3653

#3653 In scverse/scanpy;

· flying-sheep opened on May 28, 2025

Column-wise <code>dask</code> <code>map_blocks</code>

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#3723 In scverse/scanpy;

· ilan-gold opened on Jul 21, 2025

Switch to <code>numpy.random.Generator</code>

Area – ReproducibilityExact replicationExact replication

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#3371 In scverse/scanpy;

· flying-sheep opened on Nov 18, 2024

Allow using arbitrary vectors in plotting (not only <code>obs</code> columns)

Area - Plotting 🌺

Area – APIAPI designAPI design

Status: Open.

Enhancement

#1500 In scverse/scanpy;

· picciama opened on Nov 18, 2020

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

feature request for embedding_density()

Area - Plotting 🌺

Status: Open.

Enhancement

#575 In scverse/scanpy;

· sebpott opened on Mar 30, 2019

Order of plotting datapoints with categorical colouring should be amended

Area - Plotting 🌺

Status: Open.

Enhancement

#1263 In scverse/scanpy;

· LuckyMD opened on Jun 2, 2020

Spin off read/write into it's own package?

Question

Status: Open.

#1387 In scverse/scanpy;

· adamgayoso opened on Aug 21, 2020

densmap

Status: Open.

Enhancement

#1619 In scverse/scanpy;

· ivirshup opened on Feb 2, 2021

Inline example plots in docs

Area - Documentation 📒

Area - Plotting 🌺

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

Enhancement

#1664 In scverse/scanpy;

· ivirshup opened on Feb 19, 2021

sc.pl.dotplot() <code>standard_scale='var'</code>: should scaling be changed?

Area - Plotting 🌺

Status: Open.

Enhancement

#1757 In scverse/scanpy;

· sjfleming opened on Mar 22, 2021

STARsolo Matrix with Velocyto --&gt; Anndata function

Status: Open.

Enhancement

#1860 In scverse/scanpy;

· JBreunig opened on May 27, 2021

Public function for accessing category colors

Area - Plotting 🌺

Status: Open.

Enhancement

#1881 In scverse/scanpy;

· brianpenghe opened on Jun 17, 2021

leiden and umap not reproducible on different CPUs

Area - Documentation 📒

Area – ReproducibilityExact replicationExact replication

Status: Open.

Enhancement

#2014 In scverse/scanpy;

· grst opened on Oct 15, 2021

Compute UMAP from pre-existing distance matrix

Area - Topology 🍩Neighbor graphsNeighbor graphs

good first issueeasy first issue to get started in OSS community contribution!easy first issue to get started in OSS community contribution!

Status: Open.

Enhancement

#2157 In scverse/scanpy;

· ivirshup opened on Feb 25, 2022

Remove <code>sc.external</code>

Area – APIAPI designAPI design

Area – ExternalDealing with external toolsDealing with external tools

MetaA meta-request to be implemented in multiple stepsA meta-request to be implemented in multiple steps

Status: Open.

#2717 In scverse/scanpy;

· flying-sheep opened on Oct 26, 2023

Option to return sparse arrays from <code>sc.get.aggregate</code>

Area – APIAPI designAPI design

Status: Open.

Enhancement

#2898 In scverse/scanpy;

· ivirshup opened on Mar 6, 2024

Get modularity score after community detection in leiden/louvain

Status: Open.

Enhancement

#2908 In scverse/scanpy;

· AlSzmigiel opened on Mar 13, 2024

cluster cells within groups when plotting with scanpy.pl.heatmap()

Area - Plotting 🌺

Status: Open.

Enhancement

#3129 In scverse/scanpy;

· zsfrbkv opened on Jun 28, 2024

feature selection method using pearson residuals discrepancies

Question

Status: Open.

Bug

#3452 In scverse/scanpy;

· jflucier opened on Jan 24, 2025

replace remaining utils with fast-array-utils

Development Process 🚀

Status: Open.

Enhancement

#3784 In scverse/scanpy;

· flying-sheep opened on Sep 4, 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