Giovanni Palla

gimVI gene imputation error

1

the `get_imputed_values` method from gimvi not working? ```python from scvi.external import GIMVI GIMVI.setup_anndata(adata_sp_train, layer="counts") GIMVI.setup_anndata(adata_sc, layer="counts") model = GIMVI(adata_sc, adata_sp_train) model.train(10, batch_size=256) imputed = model.get_imputed_values(normalized=True, batch_size=256) ``` ```pytb --------------------------------------------------------------------------- ValueError...

## Description ... ## Minimal reproducible example ```python ... ``` ## Traceback ```pytb ... ``` ## Version ...

text from zulip from phil https://results.pre-commit.ci/. The link there e.g. leads to https://github.com/apps/pre-commit-ci/installations/23763214

`sc.pl.spatial` alpha values for continuos/discrete annotations

6

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

clustering accounting for spatial coordinates

12

Not very clear idea, but something along these lines: https://www.biorxiv.org/content/10.1101/2020.09.04.283812v1 Maybe a way to achieve similar results without explicit modelling and inference. It's essentially a smoothing of cluster assignments on...

External module

2

### Type of the feature - [ ] New function in `sqduipy.im`? - [ ] New function in `squidpy.gr`? - [ ] New function in `squidpy.pl`? - [ ] Change...

Visualization gene expression by distance

5

### Type of the feature - [ ] New function in `sqduipy.im`? - [x] New function in `squidpy.gr`? - [x] New function in `squidpy.pl`? - [ ] Change an existing...

Use radius graph for co-occurrence score

1

## Description The way we are doing the co-occurrence score is really ugly and it should be rewritten. We should remove the euclidean distance and use the graph computed with...

why enforce lowercase?

4

https://github.com/broadinstitute/Tangram/blob/3c87a25d49ad50b7f85ba68c67d31b46e38c3847/tangram/mapping_utils.py#L40-L41 think it'd be useful if this operation is optional.

first attempt to support awkward arrays

43

First draft at supporting [awkward arrays](https://awkward-array.org/quickstart.html#). As discussed with @ivirshup this would be useful for Squidpy @hspitzer (discussed also here #609 ) and potentially @Zethson EHR project. Here's a walkthrough...