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gu-lab20 / MD-ALL

Molecular Diagnosis (MD) of Acute Lymphoblastic Leukemia (ALL): An integrative ALL classification system based on RNA-seq.
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Cell types deconvolution info #4

Open albertop210 opened 1 year ago

albertop210 commented 1 year ago

Hi authors, Compliments for the great tool! Reading the paper in which you present MD-ALL I focused on the deconvolution of bulk RNAseq data using CIBERSORTx and a custom single cell reference. I understood that you re-performed filtering on a 166K cells matrix from 1-Million Immune Cells Project; how did you obtain the final reference matrix? Did you loaded it in a repo or database or is it accessible? I would also like to perform some tests on deconvolution and try to use different reference matrices. Thanks a lot in advance for our help.

Alberto

gu-lab20 commented 3 months ago

Hi Alberto,

We did a manual selection based on the cell markers of each cell type in the original dataset. All the reference data are in the data folder in .rda format. https://github.com/gu-lab20/MD-ALL/blob/master/data/SE_celltype.rda should be the one you need. You can read it into R.