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aertslab / scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
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Integration of multiple single-cell multiomics samples for GRN construction #191

Closed Ajeet1699 closed 1 year ago

Ajeet1699 commented 1 year ago

Hi,

Thanks for building the wonderful tool. I have multiple single cell multiomics (same cells) samples (6 diseased and 6 control individuals) and I want to construct single GRN for each cell type. I am following "https://scenicplus.readthedocs.io/en/latest/pbmc_multiome_tutorial.html"which I understand was run only on one sample. What is the best way to integrate the multiple samples (cell ranger aggr or by Seurat) for building GRN? I can build an integrated .h5 object for scRNA seq data but for ATAC, there are separate "atac_fragments.tsv" files for each samples, how to handle these?

And I am also wondering that will I have to build the separate GRNs for diseased and control samples? or is these a way to compare these in Scenic+?

Thanks in advance