search

Teichlab / cellphonedb

MIT License
338 stars 105 forks source link

bulk RNA-SEQ dataset #300

Closed bioguy2018 closed 3 years ago

bioguy2018 commented 3 years ago

Dear developers, Can CellphoneDB in principal be applied to bulk rna-seq data? if yes what I should bear in mind for the analysis

Thank you

jariwalask commented 3 years ago

How are you planning on defining clusters? Cell types through deconvolution?

bioguy2018 commented 3 years ago

Hi, My cell types are already defined prior to the experiment. I have two set of samples each belonging to a different cell type and they have been sequenced.

luzgaral commented 3 years ago

Hi,

CellphoneDB requires single-cell unit. You will need to find a way to move from your cell type-specific bulk data to a single cell-like dataset.

One option is to consider each replicate in each set of samples as a pseudo single cell. Bear in mind that you will need a few replicates as in single cell we expect at least 50 cells per cell type.

Hope this helps,

Luz