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Allow users to pass inner to sc.pl.violin when multi_panel=True

Area - Plotting 🌺

Status: Draft (not ready).

scverse/scanpynumber 2083

#2083 In scverse/scanpy;

· ivirshup opened on Dec 14, 2021

Added intercept to regress_out()

Status: Open (in progress).

scverse/scanpynumber 2731

#2731 In scverse/scanpy;

· ggit12 opened on Nov 6, 2023

obs. vs. obs for all grouped plots using <code>BasePlot</code>

Status: Open (in progress).

scverse/scanpynumber 2769

#2769 In scverse/scanpy;

· yugeji opened on Nov 28, 2023

Generalize tl.dendrogram function to either axis

Status: Open (in progress).

scverse/scanpynumber 2771

#2771 In scverse/scanpy;

· dburkhardt opened on Nov 28, 2023

DensMAP support

Status: Open (in progress).

scverse/scanpynumber 2946

#2946 In scverse/scanpy;

· keller-mark opened on Mar 22, 2024

Start overhaul for embedding sort order

Status: Draft (not ready).

scverse/scanpynumber 2998

#2998 In scverse/scanpy;

· ivirshup opened on Apr 10, 2024

feat: add layer argument for sc.tl.score_genes_cell_cycle

Status: Open (in progress).

scverse/scanpynumber 3138

#3138 In scverse/scanpy;

· shinthor opened on Jul 2, 2024

✨ Add colorblocks to baseplot similar to heatmap

Area - Plotting 🌺

Status: Open (in progress).

scverse/scanpynumber 3043

#3043 In scverse/scanpy;

· mbuttner opened on May 2, 2024

Draft PR: Add modularity and modularity_adata functions to scanpy.metrics

Status: Open (in progress).

scverse/scanpynumber 3613

#3613 In scverse/scanpy;

· amalia-k510 opened on Apr 25, 2025

Add neighbors_from_distance for computing neighborhood graphs from precomputed distance matrices

Status: Open (in progress).

scverse/scanpynumber 3627

#3627 In scverse/scanpy;

· amalia-k510 opened on May 8, 2025

Remove external tests and deprecate sc.external

Status: Draft (not ready).

scverse/scanpynumber 3645

#3645 In scverse/scanpy;

· flying-sheep opened on May 26, 2025

_sparse_nanmean is inefficient

Area – Performance 🐌

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

#1894 In scverse/scanpy;

· ivirshup opened on Jun 22, 2021

<code>sc.external.pp.magic</code>: what is <code>n_jobs</code>'s default _really_?

Status: Open.

#2387 In scverse/scanpy;

· alexlenail opened on Dec 27, 2022

Refactor <code>BasePlot</code> not to create a dataframe representation of the data

Area - Plotting 🌺

Area – Performance 🐌

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

#3718 In scverse/scanpy;

· ilan-gold opened on Jul 18, 2025

docs: document array type support

Status: Open (in progress).

scverse/scanpynumber 3895

#3895 In scverse/scanpy;

· flying-sheep opened on Nov 14, 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

feat: allow <code>use_graph</code> for metrics

Status: Open (in progress).

scverse/scanpynumber 3898

#3898 In scverse/scanpy;

· flying-sheep opened on Nov 18, 2025