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.
Follow changes in the release notes.
scVelo on the cover of Nature Biotechnology 2020-12-01¶
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
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.
Workarounds for some changes/ bugs in pandas 1.3 PR 1918 I Virshup
Fixed bug where
sc.pl.paga_comparecould mislabel nodes on the paga graph PR 1898 I Virshup
normarguments 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
trikua feature selection method to the ecosystem page PR 1722 AM Ascensión
progenyto the ecosystem page PR 1767 P Badia-i-Mompel
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
Reorganized reference docs PR 1753 I Virshup
Fixed typos in grouped plot doc-strings PR 1877 C Rands
Fix detection of whether IPython is running PR 1844 I Virshup
Fixed errors and warnings from embedding plots with small numbers of categories after
sns.set_palettewas called PR 1886 I Virshup
Fixed handling of
gene_symbolsargument in a number of
sc.pl.rank_genes_groups*functions PR 1529 F Ramirez I Virshup
Fixed handling of
.rawis present PR 1895 I Virshup