Kai Waldrant

reticulate 1.36 breaks anndata R

3

Anndata throws an error when trying to access for example `.obs`: `Error: Expected a python object, received a character` Might be related to rstudio/reticulate#1531

Add novel method to predict modality task

2

## Describe your changes ## Issue ticket number and link Closes #xxxx (Replace xxxx with the GitHub issue number) ## Checklist before requesting a review - [x] I have performed...

## Describe your changes ## Issue ticket number and link Closes #xxxx (Replace xxxx with the GitHub issue number) ## Checklist before requesting a review - [ ] I have...

[predict_modality] add Simple MLP from Neurips 2021

1

## Describe your changes ## Issue ticket number and link Closes #xxxx (Replace xxxx with the GitHub issue number) ## Checklist before requesting a review - [ ] I have...

[bat_int] hcla dataset cannot be processed

1

**Describe the bug** Processing the cellxgene dataset `hcla` with the batch integration dataset processor an error is raised: ```bash Traceback (most recent call last): File "/tmp/nxf.DNtRDk7Ba7/.viash_script.sh", line 60, in adata_with_hvg...

Migration of the multi modality - Joint embedding task from neurips 2021 to openproblems v2

**Describe the bug** When trying to normalize the `human_retina_cell_atlas` dataset an error is raised: ```bash Traceback (most recent call last): File "/tmp/nxf.AI6Hw8VUNe/.viash_script.sh", line 43, in lognorm = sc.pp.log1p(norm["X"]) File "/usr/local/lib/python3.10/functools.py",...

[bat_int] cell cycle genes not in adata for cellxgene_census dataset

3

**Describe the bug** The Metric `cell_cycle_conservation` fails with datasets from the Cell x Gene Census: ``` ValueError: cell cycle genes not in adata organism: human varnames: ['ENSG00000105792', 'ENSG00000128253', 'ENSG00000015413', 'ENSG00000164402',...

**Describe the bug** `numpy.core._exceptions._ArrayMemoryError: Unable to allocate 56.0 GiB for an array with shape (301796, 24923) and data type float64` **To Reproduce** Steps to reproduce the behavior: 1. Go to...