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May i ask 1 question:
if data is already pseudobulk object from scRNAseq data with logCPM value, how can i change it back to a seurat object with counts value? Can i still use above method to turn …
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Hi,
Thank you for this helpful tool!
I found it very slow to run on a single 10x scRNAseq dataset. I used 16 cores. After almost three days, I only get chr3.bed after generating`_split.sorted.bed.…
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Do marker genes from sc show "pure" signal in ST?
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While creating environment I get the following error: Can you please help?
```
pipenv install
Creating a virtualenv for this project...
Pipfile: /home/subudhak/Documents/zena_scrnaseq_singleR/ex…
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Thanks a lot for making all data available here.
I have a question on matching in the "SpatialNF/examples/data" folder. How can I match the cells in _mouse_cortex_molecular_cartography_ to the cell…
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Hi,@zzhu33
I am trying to use scSplitter to split my 10X scRNAseq data, but I met an error "ERROR -2:invalid number of input files: 1 ".Would you please help me with this problem?
**Following are…
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Hello! Very interesting paper! I am curious about trying this method out but I wanted to ask a couple questions first:
1. Based on your supplemental table 1, you show the number of cells coming …
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I receive a segfault when I try to run
/home/cdieterich/software/STARdevelop/STAR --runThreadN 10 --genomeDir ${INDEX} --genomeLoad NoSharedMemory --readFilesCommand zcat --readFilesPrefix ${fastq_di…
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hello!
Thank you for your perfect tutorial! I am a new hand about scRNAseq and I have a question about the value which repesents the expression of gene. In my opinion, the UMI counts matrix obtained…
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Hello,
I'm interested in visualizing read distribution for specific cells/clusters from scRNAseq data. Is there a method to generate a pseudoalignment bam/sam file from kb outputs to view via IGV? …