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: anndata overhaul, diverse contributions ☀

• Gökcen Eraslan: diverse contributions ☀

• Sergei Rybakov: diverse contributions ☀

• Fidel Ramirez: plotting ☀

• Tom White: distributed computing

• Philipp Angerer: initial anndata conception/development, software quality ☀

• Alex Wolf: initial anndata & scanpy conception/development ☀

• 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.

• If Scanpy is useful for your research, consider citing Genome Biology (2018).

• Follow changes in the release notes.

• Find tools that harmonize well with anndata & Scanpy via the external API and the ecosystem page.

News - CZI grant 2019-11-14

Scanpy has been selected an essential open source software for science by CZI among 32 projects, along with giants such as Scipy, Numpy, Pandas, Matplotlib, scikit-learn, scikit-image/plotly, pip, jupyterhub/binder, Bioconda, Seurat, Bioconductor, and others.

Latest release

1.4.6 2020-03-17

Functionality in external

• sam() self-assembling manifolds [Tarashansky19] PR 903 A Tarashansky

• harmony_timeseries() for trajectory inference on discrete time points PR 994 A Mousa

• wishbone() for trajectory inference (bifurcations) PR 1063 A Mousa

Code design

• violin now reads .uns['colors_...'] PR 1029 michalk8

Bug fixes

• adapt ingest() for UMAP 0.4 PR 1038 PR 1106 S Rybakov

• compat with matplotlib 3.1 and 3.2 PR 1090 I Virshup, P Angerer

• fix PAGA for new igraph PR 1037 P Angerer

• fix rapids compat of louvain PR 1079 LouisFaure

1.4.5 2019-12-30

Please install scanpy==1.4.5.post3 instead of scanpy==1.4.5.

New functionality

• ingest() maps labels and embeddings of reference data to new data → tutorial: integrating-data-using-ingest PR 651 S Rybakov, A Wolf

• queries recieved many updates including enrichment through gprofiler and more advanced biomart queries PR 467 I Virshup

• set_figure_params() allows setting figsize and accepts facecolor='white', useful for working in dark mode A Wolf

Code design

• downsample_counts now always preserves the dtype of it’s input, instead of converting floats to ints PR 865 I Virshup

• allow specifying a base for log1p() PR 931 G Eraslan

• run neighbors on a GPU using rapids PR 850 T White

• param docs from typed params P Angerer

• embedding_density() now only takes one positional argument; similar for embedding_density(), which gains a param groupby PR 965 A Wolf

• webpage overhaul, ecosystem page, release notes, tutorials overhaul PR 960 PR 966 A Wolf

Warning

• changed default solver in pca() from auto to arpack

• changed default use_raw in score_genes() from False to None