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Dear BLAZE developers,
I was wondering if the BLAZE pipeline can be used with a different single-cell protocol than 10X.
If our single-cell protocol has a different Adapter sequence, and we have …
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Hello, I am a TRUST4 beginner, so the questions may be quite basic. I hope you can patiently answer them.
In my studies, I encountered some situations where when I read a directly downloaded Bam file…
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Hello,
Thanks for this package. I have a few quenstions about the data processing. For the droplet-based method, why we need to perform cellranger to obtain bam files and then use STARsolo? Can we…
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Hi Luyi,
The pipeline is great! Thanks for the effort and for sharing it.
I have tried FLAMES on your published data and our own in-house data, and have two questions:
1) For match_cell_barco…
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Dear Alex:
My name is Chen Weng, I'm a postdoc at Whitehead Institute. Thank you for the amazing tool!
We have some dataset that has very long "Cell barcode", up to 43bp. When I try to…
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Hi!
I'm having an issue with the export_pseudobulk function, which has been previously [41](https://github.com/aertslab/pycisTopic/issues/41). The function runs but doesn't output any files and in…
SITRR updated
3 months ago
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Hello everyone,I'm trying to conduct a mapping of my 10x scRNA-seq data with a customized reference genome using STARsolo.My analysis seemed to work properly ("finished successfully" message appeared)…
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Hello,
Thanks again for creating this nice package! I want to let you know that It has been instrumental to build up a paper that will be soon published in Nature Communications (and your software …
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Hi!
I'm getting a crash when running emptyDropsCellRanger.
The call:
```
DropletUtils::emptyDropsCellRanger(dge)
```
Where dge is a matrix of cells by genes. I'll note this data set is comp…
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Hello,
Terrific package, started using in October 2023. I've hit a few snags with the latest release (new install) with MetadataPlot, I'll post a separate issue.
With respect to feature extracti…