Can I use this with counts tables and without the cellranger, scanpy, seurat, etc. input?

bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data

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Can I use this with counts tables and without the cellranger, scanpy, seurat, etc. input? #22

Open jolespin opened 2 years ago

jolespin commented 2 years ago

I have a bunch of single-celled transcriptomes that I mapped to hg38.p13 GENCODE v39. I have counts with respect to Ensembl gene ids and also have them for gene name.

I'm looking through the tutorial and I'm not sure if I have everything to run this. Call this X.tsv.gz

I also have cell-type markers that I downloaded from PanglaoDB. Call this cell-type_markers.tsv.gz

How can I structure my data so I can use this tool?

bioinfo-ibms-pumc commented 1 year ago

You can format you markers with two columns like the 'user.table' file. Then use this file to annotate your markers. You should also prepare your input file in format from seurat or other softwares like the 'seurat*.csv' listed in SCSA resource.