Michaela Müller

Splice types

1

Annotate Splicing outputs with different splice types.

Speedup FRASER couting on Cluster

1

Copy BAM files to local `resources.tmpdir` for faster processing. This would probably require Snakemake>=6.0

Bugfix: Gene score edge case where gene_list gene is chosen as control gene

6

In some edge cases, the control gene selection retrieves the same gene(s) that are also in the gene_list used for scoring. As a result, when the following line is called,...

### Please make sure these conditions are met - [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on...

Error fitting pystan model

10

I'm getting an error when calling the pipeline through singularity with the test data that was [provided in the README](https://github.com/wheaton5/souporcell#practicetesting-data-set-demuxlet-paper-data). The issue persists when I use a local installation of...

AttributeError: 'Liger' object has no attribute 'var_genes'

3

I'm getting the following error when trying to run the `scale_not_center` function Traceback (most recent call last): File "/tmp/viash-run-pyliger-hnRbbi.py", line 45, in pyliger.scale_not_center(lobj) File "/usr/local/lib/python3.10/site-packages/pyliger/preprocessing/_scale.py", line 47, in scale_not_center var_gene_idx...

Error reading zarr file

1

**Describe the bug** Getting the following error when trying to read a zarr file ``` /hpc/projects/hca_integration/workspace/hca_pipelines/workflow/metrics/.snakemake/conda/152006085908115996d5d904bffd05fa_/lib/python3.9/site-packages/mudata/_core/mudata.py:491: UserWarning: Cannot join columns with the same name because var_names are intersecting. warnings.warn( /hpc/projects/hca_integration/workspace/hca_pipelines/workflow/metrics/.snakemake/conda/152006085908115996d5d904bffd05fa_/lib/python3.9/site-packages/mudata/_core/mudata.py:491:...

Revising open problem task structure

1

**Is your feature request related to a problem? Please describe.** After looking over the [task structure](https://openproblems.bio/documentation/create_task/task_structure#fig-task-workflow) again, I feel like it might be somewhat restrictive to a certain type of...

Adding more data from Cell Census for batch integration

1

Dataset overview: https://docs.google.com/spreadsheets/d/13HwfaqKsKPhha1pCWFM3K-8Z2HL8B1EcqultOjFeX5E/edit#gid=0