sanbomics_scripts
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mousepixels
scripts and notebooks from sanbomics
I'm trying to construct the reference for Salmon, but the process stopped with this error: salmon index -t CRCH38_and_decoys.fa.gz -d decoys.txt -i GRCh38_salmon_index --gencode [2024-02-19 12:14:55.227] [puff::index::jointLog] [warning] Entry with...
Hi @mousepixels I'm trying to read this GEO dataset (GSE198896) and I can't load it using Scanpy's adata function. The file in CSV format is not provided. In this case,...
Hi Mark, I have a question. I am doing differential expression between two cell types in scRNA-seq, I tried scVI and it worked but diffxpy did not worked, it gives...
hello all, I've written the following code reference your [youtube](https://www.youtube.com/watch?v=como93CmnS8) video: However I get the following error when I try to load it into R using using ```Read10X``` from seurat:...
Hi, I was testing your tutorial on pseudobulk with pseudo replicates and I noticed that all the replicates created by your script are identical because you did not slice with...
Hi, thank you a lot for your SoupX tutorial. I find the video and the code very helpful during my own analysis since I am new to scRNAseq analysis. One...
Hello, I am new to bioinformatics and in R and from wet lab background. I am analyzing three single cell multiomics (RNA + ATAC) datasets from 10x genomics. When I...
### Why: In the integration section, we looped through all of the csv files and saved the sample names in `adata.obs['Sample']`. However, the sample name was being stored as 'raw'...
