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

• Lukas Heumos: developer, diverse contributions

• 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 1.9

1.9.0 the future

Features

• filter_rank_genes_groups() now allows to filter with absolute values of log fold change PR 1649 S Rybakov

• embedding_density() now allows more than 10 groups PR 1936 A Wolf

Version 1.8

1.8.3 the future

Docs

Bug fixes

• Fixed finding variables with use_raw=True and basis=None in scanpy.pl.scatter() PR 2027 E Rice

• Fixed scanpy.external.pp.scrublet() to address issue 1957 FlMai and ensure raw counts are used for simulation

• Functions in scanpy.datasets no longer throw OldFormatWarnings when using anndata 0.8 PR 2096 I Virshup

• Fixed use of scanpy.pp.neighbors() with method='rapids': RAPIDS cuML no longer returns a squared Euclidean distance matrix, so we should not square-root the kNN distance matrix. PR 1828 M Zaslavsky

Performance

Ecosystem

1.8.2 2021-11-3

Docs

• Update conda installation instructions PR 1974 L Heumos

Bug fixes

• Fix plotting after scanpy.tl.filter_rank_genes_groups() PR 1942 S Rybakov

• Fix use_raw=None using anndata.AnnData.var_names if anndata.AnnData.raw is present in scanpy.tl.score_genes() PR 1999 M Klein

• Fix compatibility with UMAP 0.5.2 PR 2028 L Mcinnes

• Fixed non-determinism in scanpy.pl.paga() node positions PR 1922 I Virshup

Ecosystem

• Added PASTE (a tool to align and integrate spatial transcriptomics data) to scanpy ecosystem.

1.8.1 2021-07-07

Bug fixes

• Fixed reproducibility of scanpy.tl.score_genes(). Calculation and output is now float64 type. PR 1890 I Kucinski

• Workarounds for some changes/ bugs in pandas 1.3 PR 1918 I Virshup

• Fixed bug where sc.pl.paga_compare could mislabel nodes on the paga graph PR 1898 I Virshup

• Fixed handling of use_raw with scanpy.tl.rank_genes_groups() PR 1934 I Virshup

1.8.0 2021-06-28

Metrics module

• Added scanpy.metrics module!

  • 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

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

Features

• 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

• Standardized and expanded available arguments to the sc.pl.rank_genes_groups* family of functions. PR 1529 F Ramirez I Virshup - See examples sections of rank_genes_groups_dotplot() and rank_genes_groups_matrixplot() for demonstrations.

• scanpy.tl.tsne() now supports the metric argument and records the passed parameters PR 1854 I Virshup

Ecosystem

• Added Cubé to ecosystem page PR 1878 C Lambden

• 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

Documentation

• Added Community page to docs PR 1856 I Virshup

• Added rendered examples to many plotting functions issue 1664 A Schaar L Zappia bio-la L Hetzel L Dony M Buttner K Hrovatin F Ramirez I Virshup LouisK92 mayarali

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

• • Reorganized reference docs PR 1753 I Virshup

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

• Fixed typos in grouped plot doc-strings PR 1877 C Rands

• Extended examples for differential expression plotting. PR 1529 F Ramirez - See rank_genes_groups_dotplot() or rank_genes_groups_matrixplot() for examples.

Bug fixes

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

• Fix detection of whether IPython is running PR 1844 I Virshup

• Fixed reproducibility of scanpy.tl.diffmap() (added random_state) PR 1858 I Kucinski

• Fixed errors and warnings from embedding plots with small numbers of categories after sns.set_palette was called PR 1886 I Virshup

• Fixed handling of gene_symbols argument in a number of sc.pl.rank_genes_groups* functions PR 1529 F Ramirez I Virshup

• Fixed handling of use_raw for sc.tl.rank_genes_groups when no .raw is present PR 1895 I Virshup

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

Development processes

• Switched to flit for building and deploying the package, a simple tool with an easy to understand command line interface and metadata PR 1527 P Angerer

• Use pre-commit for style checks PR 1684 PR 1848 L Heumos I Virshup

Deprecations

• Dropped support for Python 3.6. More details here. PR 1897 I Virshup

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

• Deprecated MulticoreTSNE backend for scanpy.tl.tsne() PR 1854 I Virshup