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.

Key Contributors

anndata graph | scanpy graph | ☀ = maintainer

• 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 1.8

1.8.0 the future

Features

• Switched to flit for building and deploying the package, a simple tool with an easy to understand command line interface and metadata.

• Added layer and copy kwargs to normalize_total() PR 1667 I Virshup

• Added vcenter and norm arguments to the plotting functions PR 1551 G Eraslan

Metrics module

• Added scanpy.metrics module!

  • Added scanpy.metrics.confusion_matrix() for comparing labellings PR 915 I Virshup

  • Added scanpy.metrics.gearys_c() for spatial autocorrelation PR 915 I Virshup

  • Added scanpy.metrics.morans_i() for global spatial autocorrelation PR 1740 I Virshup, G Palla

External tools

Performance enhancements

Bug fixes

• Fix scanpy.pl.paga_path() TypeError with recent versions of anndata PR 1047 P Angerer

Deprecations

• Deprecated layers and layers_norm kwargs to normalize_total() PR 1667 I Virshup

Documentation

• Clarified docs issues for neighbors(), diffmap(), calculate_qc_metrics() PR 1680 G Palla

• Integrated DocSearch, a find-as-you-type documentation index search. PR 1754 P Angerer

Version 1.7

1.7.3 the future

Performance enhancements

Bug fixes

• scanpy.pl.rank_genes_groups_violin() now works for raw=False PR 1669 M van den Beek

Deprecations

Documentation

Ecosystem

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 scanpy.external.pp.scvi PR 1554 G Xing

• Updated default params of sam() to work with larger data PR 1540 A Tarashansky

Documentation

• New contribution guide PR 1544 I Virshup

• zsh installation instructions PR 1444 P Angerer

Performance

• Speed up read_10x_h5() PR 1402 P Weiler

• Speed ups for obs_df() PR 1499 F Ramirez

Bugfixes

• Consistent fold-change, fractions calculation for filter_rank_genes_groups PR 1391 S Rybakov

• Fixed bug where score_genes would error if one gene was passed PR 1398 I Virshup

• Fixed log1p inplace on integer dense arrays PR 1400 I Virshup

• Fix docstring formatting for rank_genes_groups() PR 1417 P Weiler

• Removed PendingDeprecationWarning`s from use of `np.matrix PR 1424 P Weiler

• Fixed indexing byg in ~scanpy.pp.highly_variable_genes PR 1456 V Bergen

• Fix default number of genes for marker_genes_overlap PR 1464 MD Luecken

• Fixed passing groupby and dendrogram_key to dendrogram() PR 1465 M Varma

• Fixed download path of pbmc3k_processed PR 1472 D Strobl

• Better error message when computing DE with a group of size 1 PR 1490 J Manning

• Update cugraph API usage for v0.16 PR 1494 R Ilango

• Fixed marker_gene_overlap default value for top_n_markers PR 1464 MD Luecken

• Pass random_state to RAPIDs UMAP PR 1474 C Nolet

• Fixed anndata version requirement for concat() (re-exported from scanpy as sc.concat) PR 1491 I Virshup

• Fixed the width of the progress bar when downloading data PR 1507 M Klein

• Updated link for moignard15 dataset PR 1542 I Virshup

• Fixed bug where calling set_figure_params could block if IPython was installed, but not used. PR 1547 I Virshup

• violin() no longer fails if .raw not present PR 1548 I Virshup

• spatial() refactoring and better handling of spatial data PR 1512 G Palla

• pca() works with chunked=True again PR 1592 I Virshup

• ingest() now works with umap-learn 0.5.0 PR 1601 S Rybakov