Can BayesPrism be used to deconvolute normal and disease muscle tissues to different cell types?

[guodudou2]

Hello,

I am interested to deconvolute muscle tissues (non-tumor) bulk RNAseq data to muscle fiber subtypes, adipose cell and immune cell proportions and cell type specific expression matrix.

Do you think BayesPrism can be used for this purpose? What reference data should I prepare as input?

Thank you very much, Wendy

[tinyi]

Hi Wendy,

Yes. BayesPrism works for both tumor and non-tumor datasets. Many of the benchmarks in our manuscript were done on non-tumor datasets, such PBMC and brain cells. Simply set key=NULL when constructing the prism object. Please refer to the vignette for details.

Best,

Tinyi

On Mon, Jan 15, 2024 at 5:31 PM guodudou2 @.***> wrote:

Hello,

I am interested to deconvolute muscle tissues (non-tumor) bulk RNAseq data to muscle fiber subtypes, adipose cell and immune cell proportions and cell type specific expression matrix.

Do you think BayesPrism can be used for this purpose? What reference data should I prepare as input?

Thank you very much, Wendy

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[guodudou2]

Hi Tinyi,

Thanks for the feedback and suggestion. Will look into it!

Best, Wendy