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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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how can I start the single cell RNA seq analysis with Giotto Suite based on the differential gene expression results #532

Closed xhNorthwestern closed 1 year ago

xhNorthwestern commented 1 year ago

Hi,

Recently I tried to use Giotto Suite to do single cell RNA seq data analysis. I obtained the data from one published paper, but my analysis results are not consistent with the figures in the paper, especially cluster number and cluster annotation. Later I found their DGE data including four files, barcodes_anno.csv, dge.csv, gene.csv and markers.csv. Can I reproduce the paper results with these four files? Could you give me some suggestions on how I start the analysis with these files?

I really appreciate your help! Many thanks!

RubD commented 1 year ago

Hi @xhNorthwestern

It's hard to provide suggestions since we don't really know how the data looks like. You can in theory use Giotto as a scRNA-seq data analysis tool, but at minimum you'll need to have gene expression matrix with raw and/or normalized counts.

Best, Ruben