Generation of Gene Expression Matrix for Scenic when starting with Cell Ranger

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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Generation of Gene Expression Matrix for Scenic when starting with Cell Ranger #206

Closed sylestiel closed 2 years ago

sylestiel commented 3 years ago

Hi,

     Having read in the 10x Cell Ranger output how do we proceed to generate the exprMat if what we have is a sparse Matrix of class "dgCMatrix"?

Do we run part of the assay using Seurat before going into Scenic?

Also can we use Multiomic scATAC+GEX data from Cell ranger to process it in Scenic?

Thanks!

s-aibar commented 2 years ago

Dear @sylestiel ,

We are working on a pipeline that will allow to analyze simultaneously gene expression and scATAC data, but it is not public yet. Feel free to follow https://github.com/aertslab to get notified of updates...

Regards