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Dear cellatac devs,
When running cellatac on a single sample of my cellranger-arc mapping output I'm running into the following error during the clustering step of the script (specifically at this …
egerc updated
2 months ago
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I'm getting the following error:
```
2024-04-18 15:45:14.641 cgjobinfo_jobid: 20748
2024-04-18 15:45:14.642 ==================== sc_filter_default_scisoformfile10x-isoquant_sc-sminimap2_splice-ba…
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Hi,
I just want to say that I've read your paper recently and I'm grateful for the work you've done. One discrepancy I've noticed is that there is no code provided for the QC of the fragment files.…
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From our colleagues at RCIGM, we have several example use cases related to genetic diseases. The goal is to take info about the variants and the phenotypes, and to propose candidate therapies. For t…
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Longitudinal 16S dataset:
Justin D. Silverman et al 2018. [Dynamic linear models guide design and analysis of microbiota studies within artificial human gut](https://microbiomejournal.biomedcentral.…
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### The motivation
(This is a specific problem that involves large-scale x-bte refactoring. Let's discuss the "large issues" of x-bte refactoring one at a time.)
When writing x-bte operations, t…
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[TEXT HERE]
```python
scvi.model.TOTALVI.setup_mudata(
mdata,
rna_layer="counts" if rna_use_raw else None,
protein_layer="counts" if protein_use_raw…
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Hello,
does anyone know if it is possible to rename layers in version 5 seurat objects? I merged numerous version 5 objects in a for loop, and in doing so it seems like the layers were renamed, and…
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I have 10X multiomics data and have generated a Seurat object. Next I want to run RunAzimuth on my Seurat Object however this fails with the error mentioned in the title of this report.
Here is th…
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[paths.py](https://github.com/flatironinstitute/CaImAn/blob/e7e86411e80639c81d8ea58026660913739704f7/caiman/paths.py) lists env variables that are used to set paths (`CAIMAN_DATA` and `CAIMAN_TEMP`), …