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Dear developers,
After using `setup_sfaira`, I tried to download all human blood-related datasets by running the following command:
```
ds_blood
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Hi Shlien lab!
I am hoping you could provide example code/basic workflow on preparing cluster specific scRNAseq signatures from like a seurat object for the OTTER webapp. Finding documentation on H…
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Hi,
The TRUST4 could be used in 10X database, and whether it could be used in BD Rhapsody? If it can, whether you could tell me how it works. I will be very grateful for that.
Thanks.
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Hi, I'm interested in using this package for my scRNAseq data. Is it compatible with the SingleCellExperiment class? If so, how is this done please? (Is there a way to go from SCE to the ExpressionSet…
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Hello.
I'm trying to run SCOUT on a single sample I have from a 10X genomics run.
I have run the BAM file through the GATK recalibration steps and try to use SCOUT to call genotypes.
This is th…
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Dear all,
I am trying to apply the PISCES on my own scRNAseq data. However, I have been stuck about how to generate the ARACNe network in the same format as the cbmc-network you provided in the vig…
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Hi,
I am trying to use shapeit5 for the first time. I tested the "test" script and it works.
I am getting this error for the output file
`ESC[31mERROR: ESC[0mFilename extension of [/phased_chr/pha…
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Hi all,
first thank you for creating this amazing tool! We transplant human cells into mouse tissue and perform scRNAseq. I would like to look at communication between mouse and human species. Cou…
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### Description of feature
Just wanted to put it down and mention that I am currently working on the implementation of cellranger-arc (modules + subworkflow). Maybe worth to discuss if this is fine t…
heylf updated
8 months ago
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Hello ! When I use this code: SEVtras.sEV_recognizer(input_path='./', sample_file='./skin1/sample_file.txt', out_path='./skin1/
outputs', species='Homo')
to anylsis my 10x-scRNAseq raw file, after…