Lukas Heumos comments

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                                            Lukas Heumos

Verbosity Level

Dear @DarioS yes, this is too verbose. We are overhauling all notebooks in 2025 and will ensure that this is also fixed. Thank you for reading and reporting!

Milo neighborhood groups as in MiloR

Dear @MaximilianNuber would you be willing to have a go at it?

Milo neighborhood groups as in MiloR

@MaximilianNuber no worries! I'm glad to hear that you're still interested in contributing this. > Therefore the question, can I add a `glmGamPoi` class to the differential expression module to...

Milo neighborhood groups as in MiloR

Thank you! I read everything but will only respond to a few things: 1. Can we make `formulaic_constrasts` an optional dependency that is only imported when needed? https://github.com/scverse/pertpy/blob/main/pyproject.toml#L77 it's already...

Milo neighborhood groups as in MiloR

No worries! I'm very grateful for your contribution and we'll figure things out together :)

Update ATAC-seq section with: Benchmarking computational methods for single-cell chromatin data analysis

Thank you, will do!

Adding tables + improve structure of strengths and limitations

Yes! I'm all for it.

Instructive tutorial and discussion of feature type inference, encoding, and missingness of data

@eroell you mixed concerns here. The original issue was about DEVELOPER documentation. Now it's more about user stuff. I don't know whether we should have a new tutorial for this...

Longitudinal qc_metrics

I am generally not sure whether our QC function is any good. We might want to ask some LLMs for ideas to improve it first before simply enabling 3D etc.

revamp existing plots

The KMF implementation with holoviz. It's a pain to autogenerate that as LLMs are really stupid with holoviz. ```python import holoviews as hv import numpy as np import pandas as...