scanpy

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I think we should introduce a standardized “mask” argument to scanpy functions. This would be a boolean array (or reference to a boolean array in `obs`/ `var`) which masks out...

ivirshup

`highly_variable_genes()` with `flavor="cell_ranger"` fails there are less normalized dispersions than `n_top_genes`

1

- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [ ]...

lazappi

- [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the latest version of scanpy. - [X] (optional)...

adkinsrs

Subsample by observations grouping

12

- [X] Additional function parameters / changed functionality / changed defaults? - [ ] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...

chsher

Doc overhaul

9

This is a draft version of Furo-based scanpy docs. To finalize this PR, the furo specific changes will need to be moved to scanpydoc. Additionally, the index.rst file scanpy-tutorials needs...

adamgayoso

Fix reference links in docs

1

Links to references in docs are broken. I think we should probably switch over to [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/en/latest/) as recommended by [executable books](https://jupyterbook.org/content/citations.html).

ivirshup

Development install via conda does not work

3

- [x] I have checked that this issue has not already been reported. - [x] I have confirmed this bug exists on the latest version of scanpy. - [x] (optional)...

fbnrst

sc.pp.highly_variable does not always handle `subset` and `inplace` arguments consistently

1

Hey, while writing tests for #1715 I noted the following behavior: `output = sc.pp.highly_variable(adata,inplace=True,subset=False,n_top_genes=100)` --> Returns nothing :heavy_check_mark: --> `adata.var` fields are updated but shape stays the same :heavy_check_mark: `output...

jlause

DotPlot `.style()` resets previous value assignments

1

Multiple calls to `sc.pl.Dotplot.style()` cause resetting of parameters. This issue can be observed as a change in the default colormap shown by #1632 Other methods that set default parameters are...

fidelram

sc.tl.dendrogram doesn't use var_names

3

- [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the latest version of scanpy. - [ ]...

Fougere87