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Another option towards #304.
TCRdist3, or rather its dependency pwseqdist (MIT licensed) comes with a numba-implementation of TCRdist3 distance metrics:
https://github.com/agartland/pwseqdist/blo…
grst updated
7 months ago
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Why is `use_observed_lib_size=False` hardcoded into the LDVAE class? I.e. when specifying `use_observed_lib_size=True` in `scvi.model.LinearSCVI(...)` this leads to `TypeError: __init__() got multiple…
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### Report
I am unable to import pertpy package. The error message is linked to numpa/numpy interplay
```
Python 3.10.12 (main, Jun 21 2024, 10:35:36) [GCC 11.4.0] on linux
Type "help", "copyrig…
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### Is your feature request related to a problem?
We are looking to improve compatibility between `AnnData` and `xarray` (see https://github.com/scverse/anndata/issues/744), and so categoricals are n…
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My CI breaks for Python 3.12 because the scikit-bio dependency cannot be installed.
Here's the link to the CI run: https://github.com/scverse/scirpy/actions/runs/9697258089/job/26760987146?pr=519
…
grst updated
4 months ago
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Hi all,
I believe the napari documentation is a bit dated. Specifically, using it how it is [written here](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_napari.html), throws…
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From @quentinblampey.
Today, the version 1.9.7 of scanpy was released, but their plots are incompatible with numpy 1.23 (see here https://github.com/scverse/scanpy/issues/2830) but xarray-spatial d…
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Hi,
I have multiple samples in the same FOV in Xenium data. I am trying to subset each sample with `polygon_query`.
```
cropped = polygon_query(
sdata=sdata,
polygons=polygon,
ta…
Bo-UT updated
8 months ago
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**Error raised when running "cell2location.models.Cell2location" in analyzing multiple slides**
I was trying to mapping multiple slides multiple slides using my own snRNA and Visium data, flowing …
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When saving labels to a SpatialData that has already been written to disk (with or without `overwrite=True`), there are multiple exceptions.
### Example code
```python
import numpy as np
impor…