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.
PCA plots can now annotate axes with variance explained PR 1470 bfurtwa
External tools (new)
External tools (changes)
Consistent fold-change, fractions calculation for filter_rank_genes_groups PR 1391 S Rybakov
Fixed bug where
score_geneswould error if one gene was passed PR 1398 I Virshup
log1pinplace on integer dense arrays PR 1400 I Virshup
PendingDeprecationWarning`s from use of `np.matrixPR 1424 P Weiler
Fixed indexing byg in
~scanpy.pp.highly_variable_genesPR 1456 V Bergen
Fix default number of genes for marker_genes_overlap PR 1464 MD Luecken
Fixed download path of
pbmc3k_processedPR 1472 D Strobl
Better error message when computing DE with a group of size 1 PR 1490 J Manning
Update cugraph API usage for v0.16 PR 1494 R Ilango
marker_gene_overlapdefault value for
top_n_markersPR 1464 MD Luecken
random_stateto RAPIDs UMAP PR 1474 C Nolet
Fixed the width of the progress bar when downloading data PR 1507 M Klein
Updated link for
moignard15dataset PR 1542 I Virshup
Fixed bug where calling
set_figure_paramscould block if IPython was installed, but not used. PR 1547 I Virshup