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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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Importing CellRanger read count matrix or Seurat object into MAST #134

Closed singcell closed 4 years ago

singcell commented 4 years ago

I am analyzing data generated by 10x and CellRanger. I am comparing Control and Stimulated samples. In Seurat I create Seurat object using 10x read count matrix and use FindIntegrationAnchors and IntegrateData to integrate two conditions. I wanted to use MAST to calculate the differential expression between clusters across conditions.

I wanted to know if there is a way: 1) I can import 10x read count matrix or Seurat object to input into MAST. 2) if there is a function to import CellRanger read count matrix into MAST.

Thank you

gfinak commented 4 years ago

Doesn't Seurat allow you to use MAST as a differential expression method under the hood? https://satijalab.org/seurat/v3.0/de_vignette.html (search for MAST)

amcdavid commented 4 years ago

And if you need to convert from Seurat into MAST (or other Bioconductor packages), you can do sce = Seurat::as.SingleCellExperiment(seurat_obj) MAST::SceToSingleCellAssay(sce)

On May 7, 2020, at 12:02 PM, Greg Finak notifications@github.com wrote:

Doesn't Seurat allow you to use MAST as a differential expression method under the hood? https://satijalab.org/seurat/v3.0/de_vignette.html https://satijalab.org/seurat/v3.0/de_vignette.html (search for MAST)

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singcell commented 4 years ago

@gfinak @amcdavid Thank you