ncem

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Trouble installing on python 3.10

6

**Describe the bug** I believe this package should be installable on python 3.10, since the pyproject.toml says: ```python python = ">=3.8,

ivirshup

Hi, I would really like to try to use this method on my Xenium spatial transcriptomics data that I've pre-processed with squidpy, however Im running into some issues. Here is...

spatts14

Hi Anna, Currently, the `extend_formula_ncem` function (referenced below) computes a list of coef_couplings: ``` coef_couplings = [f"{PREFIX_INDEX}{x}:{PREFIX_NEIGHBOR}{y}" for y in cell_types for x in cell_types] ``` For my cell types,...

merelkuijs

**PR Checklist** - [x] This comment contains a description of changes (with reason) **Description of changes** I ran into deprecation erros trying to run NCEM on deconvoluted Visium data. `np.int`...

merelkuijs

**Question** Hi @AnnaChristina. In the _evaluate_per_node_type_ function, are the $r^2$ values calculated averages over all gene expression predictions for a given cell type?

showvikbiswas

Almost zero documentation for the training modules API

3

Hello, I would like to try out this package but realize there is close to zero documentation in the official 'readthedocs'/API for the train classes. Is this actually the official...

arunchakra

AnnaChristina

[DEPENDABOT]: Update sphinx-gallery requirement from <0.11,>=0.8.2 to >=0.8.2,<0.14 in /docs

1

Updates the requirements on [sphinx-gallery](https://github.com/sphinx-gallery/sphinx-gallery) to permit the latest version. Release notes Sourced from sphinx-gallery's releases. Release v0.13.0 Full Changelog Implemented enhancements: ENH: Create backreferences for default roles #1122 (StefRe)...

dependabot[bot]

[DEPENDABOT]: Update nbsphinx requirement from <0.8.7,>=0.8.1 to >=0.8.1,<0.9.3 in /docs

1

Updates the requirements on [nbsphinx](https://github.com/spatialaudio/nbsphinx) to permit the latest version. Release notes Sourced from nbsphinx's releases. nbsphinx 0.9.2 https://pypi.org/project/nbsphinx/0.9.2/ Improve support for sphinx_immaterial theme Improve support for links starting with...

dependabot[bot]

[DEPENDABOT]: Update sphinx requirement from <=4.0.0,>=3.5.4 to >=3.5.4,<=7.0.1 in /docs

1

Updates the requirements on [sphinx](https://github.com/sphinx-doc/sphinx) to permit the latest version. Release notes Sourced from sphinx's releases. v7.0.1 Changelog: https://www.sphinx-doc.org/en/master/changes.html Changelog Sourced from sphinx's changelog. Release 7.0.1 (released May 12, 2023)...

dependabot[bot]