News

Scanpy hits 100 contributors! 2022-03-31

100 people have contributed to Scanpy’s source code!

Of course, contributions to the project are not limited to direct modification of the source code. Many others have improved the project by building on top of it, participating in development discussions, helping others with usage, or by showing off what it’s helped them accomplish.

Thanks to all our contributors for making this project possible!

New community channels 2022-03-31

We’ve moved our forums and have a new publicly available chat!

Our discourse forum has migrated to a joint scverse forum (discourse.scverse.org).
Our private developer Slack has been replaced by a public Zulip chat (scverse.zulipchat.com).

Toolkit for spatial (squidpy) and multimodal (muon) published 2022-02-01

Two large toolkits extending our ecosystem to new modalities have had their manuscripts published!

Muon, a framework for multimodal has been published in Genome Biology.
Squidpy a toolkit for working with spatial single cell data has been published in Nature Methods.

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.

Scanpy featured in Nature Biotechnoloogy 2020-02-01

Single-cell RNA-seq analysis software providers scramble to offer solutions mentions Scanpy along with Seurat as the two major open source software packages for single-cell analysis [pdf].

Scanpy has been selected an “Essential open source software for science” by CZI 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.

Nature Biotechnology: A comparison of single-cell trajectory inference methods 2019-04-01

Nature Biotechnology reviews more than 70 TI tools and ranks PAGA as the best graph-based trajectory inference method, and overall, among the top 3.

Science “Breakthrough of the Year 2018” 2018-12-01

The Science “Breakthrough of the Year 2018”, Development cell by cell, mentions the first application of PAGA [^cite_plass18] among 5 papers.