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--- | ||
name: Bug report | ||
about: Cell2location doesn’t do what it should? Please help us fix it! | ||
title: '' | ||
labels: bug | ||
assignees: '' | ||
--- | ||
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- [ ] I have confirmed this bug exists on the latest version of cell2location. See https://github.com/BayraktarLab/cell2location#installation | ||
- [ ] I follow the instructions from the [scvi-tools tutorial](https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html). | ||
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**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug. | ||
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### Minimal code sample (that we can run without your data, using public data) | ||
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```python | ||
# Your code here | ||
``` | ||
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```pytb | ||
[Paste the error output produced by the above code here] | ||
``` | ||
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blank_issues_enabled: false | ||
contact_links: | ||
- name: Cell2location Community Discussions | ||
url: https://github.com/BayraktarLab/cell2location/discussions | ||
about: Ask how to solve your problem using cell2location. |
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--- | ||
name: Enhancement request | ||
about: Anything you’d like to see in cell2location? | ||
title: '' | ||
labels: enhancement | ||
assignees: '' | ||
--- | ||
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<!-- Please describe your feature you would like to see below: --> | ||
... |
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name: Usage Question | ||
about: Ask how to solve your problem using cell2location. | ||
title: '' | ||
labels: question | ||
assignees: '' | ||
--- | ||
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### Problem | ||
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<!-- Please describe your problem below: --> | ||
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- [ ] I follow the instructions from the [cell2location tutorial (using on scvi-tools)](https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html). | ||
- [ ] I have adjusted required hyperparameters to my dataset and tissue `N_cells_per_location` and `detection_alpha`. | ||
- [ ] I have provided 10X reaction/inlet as `batch_key` for reference NB regression. | ||
- [ ] I have checked [Cell2location Community Forum](https://github.com/BayraktarLab/cell2location/discussions), [scvi-tools forum](https://discourse.scvi-tools.org/) and did not find a solution | ||
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### Description of the data input and hyperparameters | ||
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<!-- Please briefly describe your : --> | ||
... | ||
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<!-- Please briefly describe your spatial data: --> | ||
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#### Single cell reference data: number of cells, number of cell types, number of genes | ||
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<!-- Please add this info: --> | ||
... | ||
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#### Single cell reference data: technology type (e.g. mix of 10X 3' and 5') | ||
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<!-- Please add this info: --> | ||
... | ||
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#### Spatial data: number of locations numbers, technology type (e.g. Visium, ISS, Nanostring WTA) | ||
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<!-- Please add this info: --> | ||
... |