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<code>sc.pp.scale</code> dask differs from csr sparse

Status: Open.

#3633 In scverse/scanpy;

· scverse-bot opened on May 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

Support obsm key to color UMAP

Status: Open.

Enhancement

#1500 In scverse/scanpy;

· picciama opened on Nov 18, 2020

Saving plots results in a prefixed filename, regardless of sc.settings.figdir

Area - Plotting 🌺

Status: Open.

Enhancement

#1508 In scverse/scanpy;

· rbpatt2019 opened on Nov 25, 2020

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

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

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

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

Dask support for pp.highly_variable_genes ("seurat_v3" flavor(s))

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

Area – Performance 🐌

Status: Open.

Enhancement

#2808 In scverse/scanpy;

· flying-sheep opened on Jan 15, 2024

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

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

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

add layer argument for sc.tl.score_genes_cell_cycle

Status: Draft (not ready).

scverse/scanpynumber 3138

#3138 In scverse/scanpy;

· shinthor opened on Jul 2, 2024

(feat): seurat v3 with dask

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

Area – Performance 🐌

Area – Preprocessing 🧼

Status: Draft (not ready).

scverse/scanpynumber 3340

#3340 In scverse/scanpy;

· ilan-gold opened on Nov 5, 2024

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