Cell types deconvolution info

[albertop210]

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]

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.