Version 1.9

1.9.8 2024-01-26

Bug fixes

• Fix handling of numpy array palettes for old numpy versions PR 2832 P Angerer

1.9.7 2024-01-25

Bug fixes

• Fix handling of numpy array palettes (e.g. after write-read cycle) PR 2734 P Angerer

• Specify correct version of matplotlib dependency PR 2733 P Fisher

• Fix scanpy.pl.violin() usage of seaborn.catplot PR 2739 E Roellin

• Fix scanpy.pp.highly_variable_genes() to handle the combinations of inplace and subset consistently PR 2757 E Roellin

• Replace usage of various deprecated functionality from anndata and pandas PR 2678 PR 2779 P Angerer

• Allow to use default n_top_genes when using scanpy.pp.highly_variable_genes() flavor 'seurat_v3' PR 2782 P Angerer

• Fix scanpy.read_10x_mtx()’s gex_only=True mode PR 2801 P Angerer

1.9.6 2023-10-31

Bug fixes

• Allow scanpy.pl.scatter() to accept a str palette name PR 2571 P Angerer

• Make scanpy.external.tl.palantir() compatible with palantir >=1.3 PR 2672 DJ Otto

• Fix scanpy.pl.pca() when return_fig=True and annotate_var_explained=True PR 2682 J Wagner

• Temp fix for issue 2680 by skipping seaborn version 0.13.0 PR 2661 P Angerer

• Fix scanpy.pp.highly_variable_genes() to not modify the used layer when flavor=seurat PR 2698 E Roellin

• Prevent pandas from causing infinite recursion when setting a slice of a categorical column PR 2719 P Angerer

1.9.5 2023-09-08

Bug fixes

• Remove use of deprecated dtype argument to AnnData constructor PR 2658 Isaac Virshup

1.9.4 2023-08-24

Bug fixes

• Support scikit-learn 1.3 PR 2515 P Angerer

• Deal with None value vanishing from things like .uns['log1p'] PR 2546 SP Shen

• Depend on igraph instead of python-igraph PR 2566 P Angerer

• rank_genes_groups() now handles unsorted groups as intended PR 2589 S Dicks

• rank_genes_groups_df() now works for rank_genes_groups() with method="logreg" PR 2601 S Dicks

• _choose_representation() now works with n_pcs if bigger than settings.N_PCS PR 2610 S Dicks

1.9.3 2023-03-02

Bug fixes

• Variety of fixes against pandas 2.0.0rc0 PR 2434 I Virshup

• Compatibility with anndata 0.9.0rc PR 2435 I Virshup

1.9.2 2023-02-16

Bug fixes

• highly_variable_genes() layer argument now works in tandem with batches PR 2302 D Schaumont

• highly_variable_genes() with flavor='cell_ranger' now handles the case in issue 2230 where the number of calculated dispersions is less than n_top_genes PR 2231 L Zappia

• Fix compatibility with matplotlib 3.7 PR 2414 I Virshup P Fisher

• Fix scrublet numpy matrix compatibility issue PR 2395 A Gayoso

1.9.1 2022-04-05

Bug fixes

• normalize_total() works when Dask is not installed PR 2209 R Cannoodt

• Fix embedding plots by bumping matplotlib dependency to version 3.4 PR 2212 I Virshup

1.9.0 2022-04-01

Tutorials

• New tutorial on the usage of Pearson Residuals: → tutorial: tutorial_pearson_residuals J Lause, G Palla

• Materials and recordings for Scanpy workshops by Maren Büttner

Experimental module

• Added scanpy.experimental module! Currently contains functionality related to pearson residuals in scanpy.experimental.pp PR 1715 J Lause, G Palla, I Virshup. This includes:

  • normalize_pearson_residuals() for Pearson Residuals normalization

  • highly_variable_genes() for HVG selection with Pearson Residuals

  • normalize_pearson_residuals_pca() for Pearson Residuals normalization and dimensionality reduction with PCA

  • recipe_pearson_residuals() for Pearson Residuals normalization, HVG selection and dimensionality reduction with PCA

Features

• filter_rank_genes_groups() now allows to filter with absolute values of log fold change PR 1649 S Rybakov

• _choose_representation now subsets the provided representation to n_pcs, regardless of the name of the provided representation (should affect mostly neighbors()) PR 2179 I Virshup PG Majev

• scanpy.external.pp.scrublet() (and related functions) can now be used on AnnData objects containing multiple batches PR 1965 J Manning

• Number of variables plotted with pca_loadings() can now be controlled with n_points argument. Additionally, variables are no longer repeated if the anndata has less than 30 variables PR 2075 Yves33

• Dask arrays now work with scanpy.pp.normalize_total() PR 1663 G Buckley, I Virshup

• embedding_density() now allows more than 10 groups PR 1936 A Wolf

• Embedding plots can now pass colorbar_loc to specify the location of colorbar legend, or pass None to not show a colorbar PR 1821 A Schaar I Virshup

• Embedding plots now have a dimensions argument, which lets users select which dimensions of their embedding to plot and uses the same broadcasting rules as other arguments PR 1538 I Virshup

• print_versions() now uses session_info PR 2089 P Angerer I Virshup

Ecosystem

Multiple packages have been added to our ecosystem page, including:

• decoupler a for footprint analysis and pathway enrichement PR 2186 PB Mompel

• dandelion for B-cell receptor analysis PR 1953 Z Tuong

• CIARA a feature selection tools for identifying rare cell types PR 2175 M Stock

Bug fixes

• Fixed finding variables with use_raw=True and basis=None in scanpy.pl.scatter() PR 2027 E Rice

• Fixed scanpy.external.pp.scrublet() to address issue 1957 FlMai and ensure raw counts are used for simulation

• Functions in scanpy.datasets no longer throw OldFormatWarnings when using anndata 0.8 PR 2096 I Virshup

• Fixed use of scanpy.pp.neighbors() with method='rapids': RAPIDS cuML no longer returns a squared Euclidean distance matrix, so we should not square-root the kNN distance matrix. PR 1828 M Zaslavsky

• Removed pytables dependency by implementing read_10x_h5 with h5py due to installation errors on Windows PR 2064

• Fixed bug in scanpy.external.pp.hashsolo() where default value was set improperly PR 2190 B Reiz

• Fixed bug in scanpy.pl.embedding() functions where an error could be raised when there were missing values and large numbers of categories PR 2187 I Virshup