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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 have been using cell chat quite a lot this past weeks for my project and I think is great.
I have some doubts on how I am supposed to be using biological replicates of the same experimen…
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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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hello, I'm using cell2cell to identify interactions with scRNAseq data.
```
interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq,
…
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Dear Dr. Li, I have encountered some problems while studying TRUST4 script commands recently. I hope to receive your guidance:
About barcoderep-filter. py, the first two lines of the report. out in m…
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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…
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Hello author,
Congratulation you got the competition deconvolution.
I just have a question naive.
For DAISM-DNN user must be have califra.txt file ?
I.e.
I have scRNAseq(.h5ad) as referen…
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@songeric1107
The colors should be consistent for the cell types between P2 and P7 for the following datasets:
- P2, mouse, scRNA-seq, cochlea (Hertzano/Ament) and P7, Mouse, cochlea, scRNAseq (H…
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Hello @YingMa0107 @YMalab > # Make CARD object
> CARD_obj = createCARDObject(
+ sc_count = sc_count,
+ sc_meta = sc_meta,
+ spatial_count = spatial_count,
+ spatial_location = spatial_l…
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Hey! I'm trying to use Assign_Indiv_by_Geno.R function of Demuxafy.sif from data of demuxlet code. It seems the problem is with the FORMAT, but I don't undestand very well...
apptainer exec Demuxaf…