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Hi Caibin,
I tried using `scar`'s output as input for TotalVI/SCVI. As expected, those gave an error because the input is not integer anymore.
I would suggest implementing stochastic rounding to i…
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Good day,
I have searched and cannot seem to find the problem I am encountering in any previous issues. I have run label transfer on my seurat object (comprising of 10 snRNAseq datasets from the t…
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Hi all,
I have a set of 10x scRNAseq (nuclei instead of cells, to be precise) datasets derived from a mouse line expressing several transgenes (sfGFP and Bgal, in this case). I only know (and only …
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Hi, I've used solo a few times now and am really appreciating how user-friendly it is. It seems to work really well on my dataset.
1. Every time I run solo, I get the following warning:
"UserWarn…
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# Please report
- [ ] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version`
Previous command results in: Error: Unable to access jarfile RNA-Bloom.jar
So command used for RNA-Bloom version…
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Thanks for this great resource! Would it be possible to add the single cell modality as a category or tag to enable further filtering of tools? E.g. scRNAseq, snRNAseq, scATACseq/multiome, CITE-seq, s…
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Hi,
I followed the Signac tutorial to merge and integrate 5 scATAC objects.
To merge, I used https://satijalab.org/signac/articles/merging.html and
I saw some batch effect. So I went ahead …
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Dear MAST team,
I would like to ask you a question..
I am using MAST for modelling gene expression in a snRNAseq data, with a random intercept for subjects identity. I am wondering if in this case, …
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### Project short name:
CerebellarDevLandscape
### Primary Wrangler:
@ipediez
### Secondary Wrangler:
### Associated files
* Google Drive: https://drive.google.com/drive/folders/1zGQpeqRoySCgX…
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HPC dissections have been performed for Br6432, Br6423, Br2743, Br2720 and Br3942. For all 5 of these brains, slides have been made for QC by H&E staining and RNAscope for the 4 subfield markers. Addi…