Scanpy – Single-Cell Analysis in Python¶

Scanpy is a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.

Isaac Virshup: lead developer since 2019 ☀
Gökcen Eraslan: developer, diverse contributions ☀
Sergei Rybakov: developer, diverse contributions ☀
Fidel Ramirez: developer, plotting ☀
Giovanni Palla: developer, spatial data
Malte Luecken: developer, community & forum
Philipp Angerer: developer, software quality, initial anndata conception ☀
Alex Wolf: lead developer 2016-2019, initial anndata & scanpy conception
Fabian Theis & lab: enabling guidance, support and environment

Discuss usage on Discourse and development on GitHub.
Get started by browsing tutorials, usage principles or the main API.
Follow changes in the release notes.
Find tools that harmonize well with anndata & Scanpy via the external API and the ecosystem page.
Consider citing Genome Biology (2018) along with original references.

News¶

scVelo on the cover of Nature Biotechnology 2020-12-01¶

Scanpy’s counterpart for RNA velocity, scVelo, made it on the cover of Nature Biotechnology [tweet].

Scanpy selected among 20 papers for 20 years of Genome Biology 2020-08-01¶

Genome Biology: Celebrating 20 Years of Genome Biology selected the initial Scanpy paper for the year 2018 among 20 papers for 20 years [tweet].

COVID-19 datasets distributed as `h5ad` 2020-04-01¶

In a joint initiative, the Wellcome Sanger Institute, the Human Cell Atlas, and the CZI distribute datasets related to COVID-19 via anndata’s h5ad files: covid19cellatlas.org. It wasn’t anticipated that the initial idea of sharing and backing an on-disk representation of AnnData would become so widely adopted. Curious? Read up more on the format.

Latest additions¶

Version 1.7¶

1.7.2 2021-04-07¶

Bug fixes

scanpy.logging.print_versions() now works when python<3.8 PR 1691 I Virshup
scanpy.pp.regress_out() now uses joblib as the parallel backend, and should stop oversubscribing threads PR 1694 I Virshup
scanpy.pp.highly_variable_genes() with flavor="seurat_v3" now returns correct gene means and -variances when used with batch_key PR 1732 J Lause
scanpy.pp.highly_variable_genes() now throws a warning instead of an error when non-integer values are passed for method "seurat_v3". The check can be skipped by passing check_values=False. PR 1679 G Palla

Ecosystem

Added triku a feature selection method to the ecosystem page PR 1722 AM Ascensión
Added dorothea and progeny to the ecosystem page PR 1767 P Badia-i-Mompel

1.7.1 2021-02-24¶

Documentation

More twitter handles for core devs PR 1676 G Eraslan

Bug fixes

dendrogram() use 1 - correlation as distance matrix to compute the dendrogram PR 1614 F Ramirez
Fixed obs_df()/ var_df() erroring when keys not passed PR 1637 I Virshup
Fixed argument handling for scanpy.external.pp.scrublet() J Manning
Fixed passing of kwargs to scanpy.pl.violin() when stripplot was also used PR 1655 M van den Beek
Fixed colorbar creation in scanpy.pl.timeseries_as_heatmap PR 1654 M van den Beek

1.7.0 2021-02-03¶

Features

Add new 10x Visium datasets to visium_sge() PR 1473 G Palla
Enable download of source image for 10x visium datasets in visium_sge() PR 1506 H Spitzer
Refactor of scanpy.pl.spatial(). Better support for plotting without an image, as well as directly providing images PR 1512 G Palla
Dict input for scanpy.queries.enrich() PR 1488 G Eraslan
rank_genes_groups_df() can now return fraction of cells in a group expressing a gene, and allows retrieving values for multiple groups at once PR 1388 G Eraslan
Color annotations for gene sets in heatmap() are now matched to color for cluster PR 1511 L Sikkema
PCA plots can now annotate axes with variance explained PR 1470 bfurtwa
Plots with groupby arguments can now group by values in the index by passing the index’s name (like pd.DataFrame.groupby). PR 1583 F Ramirez
Added na_color and na_in_legend keyword arguments to embedding() plots. Allows specifying color for missing or filtered values in plots like umap() or spatial() PR 1356 I Virshup
embedding() plots now support passing dict of {cluster_name: cluster_color, ...} for palette argument PR 1392 I Virshup

External tools (new)

Add Scanorama integration to scanpy external API (scanorama_integrate()) [Hie19] PR 1332 B Hie
Scrublet [Wolock19] integration: scrublet(), scrublet_simulate_doublets(), and plotting method scrublet_score_distribution() PR 1476 J Manning
hashsolo() for HTO demultiplexing [Bernstein20] PR 1432 NJ Bernstein
Added scirpy (sc-AIRR analysis) to ecosystem page PR 1453 G Sturm
Added scvi-tools to ecosystem page PR 1421 A Gayoso

External tools (changes)

Updates for palantir() and palantir_results() PR 1245 A Mousa
Fixes to harmony_timeseries() docs PR 1248 A Mousa
Support for leiden clustering by scanpy.external.tl.phenograph() PR 1080 A Mousa
Deprecate scvi() PR 1554 G Xing
Updated default params of sam() to work with larger data PR 1540 A Tarashansky