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Hi
When I try to run velocyto on bam file to generate a loom file, it generates the following error:
IOError("The bam file does not contain cell and umi barcodes appropriatelly formatted. If you a…
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**Page** Project
Change ordering of sections to:
The preferred order of categories
Project
Wrangling
Submission steps
Post submission tracking
We feel a need to remove the star system (can …
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Thanks for publishing your seurat object!
I took a look at the MNP-VERSE seurat object and I noticed the following things:
1. In the paper's methods section you described that 6 studies were exclu…
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**For which schema is a change/update being suggested?**
I would like to request an update to the `sequence_file.json` schema.
**What should the change/update be?** Add a field for flow cell id …
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Hi,
I believe there is an issue with the `merge` function of `Seurat`. The problem lies in the way `Seurat` handles the `feature.attributes` and `scale.data` slots of two objects with different set…
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× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [43 lines of output]
['/private/var/folders/fl/b2bz90qj3g5gvl83n8n2vpvr0000gn/T/pip-install-wlbeuffp/velocyto_5…
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Hello,
I'm looking for citation information for the panc8 dataset. When I use either the help command `?panc8` or the citation function `citation('panc8.SeuratData')` only five links are provided f…
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Hey,
Thanks for developing the SCmut tool. I am trying to use it on my own data, but my tumor- and normal- bulk bam file are all generated based on hg38. I try to use `gatk mutect2` to call somati…
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I have two data sets of single-cell transcriptomes: snrna and sprna, where snrna was obtained under Seurat v4.3 and sprna was obtained under Seurat v5. I use the same code, as shown below.
```
W3.2…
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Hi,
The data I have is just scRNA and bulk WGS. How can I obtain the somatic SNVs from SCmut? I don't have tumor sequences.
This is not cancer data, by the way.
THanks.