Lukas Heumos

### Description of feature From https://www.nature.com/articles/s41467-020-17440-w > L1000 gene expression signatures were taken from either the LINCS Phase 2 data (GEO accession GSE70138, downloaded from http://amp.pharm.mssm.edu/Slicr) or LINCS Phase 1...

### Description of feature - [ ] Adopt logging setup that @Lilly-May is implementing in ehrapy - [ ] Always note when we're adding information to the AnnData object especially...

Improve pytest speed

2

### Description of feature Currently, starting pytest takes ages because it doesn't collect the tests that fast or seems to download something. I don't really know what's going on. I...

Streamlining Distance API

5

### Description of feature This is a continuation of https://github.com/theislab/pertpy/issues/405 but specific for `Distance`. TLDR: Currently, `Distance` does not adhere to the API design of the rest of pertpy and...

### Description of feature Just with next release Also best-practices

### Description of feature We need to ensure that scgen also works well with GPUs.

Add statsmodels or pydeseq 2 support for milopy

2

Our current milo implementation uses edgeR from R to make a few calculations here: https://github.com/theislab/pertpy/blob/development/pertpy/tools/_milo.py#L310 . However, we want pertpy to be a pure Python experience. Hence, we want to...

Better support for DE in scverse

16

Continuation of a discussion in https://github.com/theislab/single-cell-best-practices/issues/141 ## Goal Implementation of useful helper methods for common DE tools. We don't plan to reimplement several DE methods. Other people are trying this...

### Description of feature I volunteered to model all cases where it works and doesn't work. Based on this we want to make an informed decision whether we can just...

ImportError: cannot import name '_get_column_indices' from 'sklearn.utils for pre-release CI in imbalanced learn

1

### Report > /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/ehrapy/__init__.py:12: in > from ehrapy import data as dt > /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/ehrapy/data/__init__.py:1: in > from ehrapy.data._datasets import ( > /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/ehrapy/data/_datasets.py:6: in > from ehrapy.io._read import read_csv, read_fhir, read_h5ad...