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.

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 [Plass18] among 5 papers.