openproblems-v2

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* [ ] Positive control method for PCR * [ ] Negative control for PCR * [ ] Negative control for ASW batch

rcannood

[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...

KaiWaldrant

The `run_benchmark` needs to be able to run methods with multiple parameter settings. Perhaps with the addition of something like this? ```yaml - name: "--parameter_sets" type: file description: | A...

rcannood

KaiWaldrant

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

KaiWaldrant

Widespread inflated metrics for label projection due to leakage

2

I was interested in the benchmarks for label projection, hoping to implement the "best" method (logistic regression) in a project. Using the example pancreas dataset, I was unable to replicate...

kthorner

### Task motivation The growing availability of single-cell data has sparked an increased interest in the inference of cell-cell communication (CCC), with an ever-growing number of computational tools developed for...

vishnu-vasan

**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",...

KaiWaldrant

rcannood

The `openproblems_v1` currently doesn't return the `feature_id` column

rcannood