Is there a vignette available on how to preprocess scRNA and scATAC seq data that is used as an input for FigR analysis?

buenrostrolab / FigR

Functional Inference of Gene Regulation

https://buenrostrolab.github.io/FigR/

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Is there a vignette available on how to preprocess scRNA and scATAC seq data that is used as an input for FigR analysis? #45

Closed yojetsharma closed 1 month ago

yojetsharma commented 4 months ago

I went through both the vignettes that are available. However, I was wondering if there was more on how to generate the .rds files for scRNA (sparsematrix) and scATAC seq (SummarizedExperiment).

vkartha commented 4 months ago

Hi there - our recommendation is to follow the initial processing and QC'ing for RNA using Seurat, and ATAC using Signac (for example), in order to get the normalized gene x cell (RNA) and peak x cell (ATAC) matrices in order. Once you've done this, you can extract the input objects for FigR analysis as mentioned in this earlier issue comment: https://github.com/buenrostrolab/FigR/issues/18#issuecomment-1385915205

Let me know if this helps