Lukas Heumos

### Description of feature perturbation space metrics

OverflowError: cannot convert float infinity to integer with ms.perturbation_signature Method in Mixscape

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### Discussed in https://github.com/theislab/pertpy/discussions/604 Originally posted by **benayedi** May 23, 2024 Hi! I'm encountering an issue when trying to run the ms.perturbation_signature method on my AnnData object. Specifically, I'm using...

scgen test broken

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### Report `FAILED tests/tools/test_scgen.py::test_scgen - flax.errors.DescriptorAttributeError: Trying to access a property that is accessing a non-existent attribute. (https://flax.readthedocs.io/en/latest/api_reference/flax.errors.html#flax.errors.DescriptorAttributeError) ` ### Version information _No response_

Expression prediction tutorial

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### Description of feature - [X] Get draft tutorial in - [ ] Add functions to pertpy - [ ] adapt tutorial with pertpy functions

Container & documentation

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Hi, would it be possible that you provide a container with a full environment to get the pipeline running, please? A small example dataset would also help a lot. Moreover,...

Forceatlas2 does not support Python 3.9+ (PAGA implementation)

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Hi, didn't see this being tracked here yet. Hope I didn't miss it. Our PAGA implementation uses Forceatlas2, but unfortunately Forceatlas2 is not really maintained anymore and it does not...

Compatibility with numpy 2.0

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Numpy 2.0 is out and lifelines currently does not support it (base requirements restrict to < 2.0). I would like to politely request an unpin if possible.

Dear maintainers, I would be happy if it were possible to move the bioconda recipe to conda-forge. Conda-forge supports: 1. More CPU architectures 2. Is more general-purpose and while Pronto...

For new term requests, please provide the following information: ## Preferred term label Vizgen MERSCOPE ## Synonyms merscope ## Textual definition Merscope is a high-resolution, in situ spatial imaging platform...

New term request visiumHD

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For new term requests, please provide the following information: ## Preferred term label Visium HD ## Synonyms visium ## Textual definition The Visium HD Spatial Gene Expression assay is a...