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Hi, thank you for the great package!
We have used this pipeline with scRNAseq data with great success.
I am wondering if it would be possible to apply TRUST4 to 10x visium data? Do we need to ma…
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Hi Aaron,
I'm currently creating an atlas of all cell types and states in a secondary lymphoid organ in the context of the Human Cell Atlas. As part of the publication, I'm preparing an R package t…
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Hi there,
I'm encountering some errors when running CellRanger with the data you provided, specifically the sample labeled 'FCA_GND8103053'. It's worth noting that I've tested the process with othe…
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Hi,
This is more naive question as I do not have experience in SNPs.
I have 2 cell-lines scRNAseq data, combined sequenced. Now would like to separate using cellSNP (& vireo).
I got bulk RNA-se…
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Hello,
Thank you for providing such a novel tool for clustering scRNAseq data.
I saw in your autoencoder python scripts that two variables are generated using the two lines below:
X_test_transf…
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Thanks so much for this incredible work!
I'd love to see (if you're adding features), options to define ground ground truths based on known marker genes, outside just `file_known_markers` — or perh…
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# General Notes
This repository serves as a mostly automated p…
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Please add metadata manifests generated by the NF Data Curator app here that have been completed, but haven't yet uploaded to Synapse. We will resolve these in an upcoming meeting:
- [ ] TEMPLATE: [M…
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@Shufeyangyi2015310117
Not getting any neighbors. Errors with code below. Can you please help?
Error with find_neighbors2():
```
Neighbors were identified for 0 out of 4221 spots.
Starti…
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Hello! I have been trying to use your tool, but when I run the TransCommuProfile function, it runs for a while, and then R freezes and I have to restart it. Do you have any ideas of why this might be …