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It is not obvious to me how to interface data loaded with `lamindb.core.MappedCollection` into an scvi model.
For example:
- initializing `adata.X` with `batch['x'] `fails because the matrix is a…
j-bac updated
7 months ago
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I wanted to start the discussion here about the docs. I will have time to work on this in the coming weeks, so it might be nice to get some agreement on (1) which framework we want to use and (2) wher…
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Using the spatialdata_io.visium_hd function to load the output of spaceranger for a visiumHD dataset can only generate an object with no shapes or tables, which cannot be directly used to plot the spa…
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The links for rendered versions of the PRs haven't been working for me for at least the last week. Does anyone know what's up with this?
I'm also wondering if this whole process could be improved b…
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## Description
...
## Minimal reproducible example
```python
import numpy as np
import scanpy as sc
import squidpy as sq
sc.logging.print_header()
print(f"squidpy=={sq.__vers…
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Hello, I believe in the current version of the "shapes by shapes" aggregation tutorial the headings for "Case: value_key referring to obs columns" and "Case: value_key referring to GeoDataFrame column…
ckmah updated
7 months ago
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Thanks for sharing this tool! It would be great if I can get some help to understand the following error:
```
Traceback (most recent call last):
File "/path/Cross Species/SATURN-main/train-saturn…
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taking inspiration from what it is done in scirpy: https://github.com/scverse/scirpy/blob/main/.github/workflows/test-tutorials.yaml
it would be useful to have a way to test the examples in CI in o…
giovp updated
7 months ago
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This issue is a starting point for discussing possible protocol extensions to allow support for various types of "awkward" arrays that do not fit into the model of arrays with fixed size dimensions an…
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When running DE on a subset of a dataset with lots of batches, seems like I need to re-index the batches of subsets so that it is consecutive from 0 ~ n_batches. Perhaps this can be done automatical…