Annotate Bulk RNASeq based on a single cell RNASeq reference

[xiw588]

Hi I wonder if it is possible and make sense to annotate Bulk RNASeq based on a single cell RNASeq reference? Thanks

[j-andrews7]

Given that most bulk samples are mixed cell types unless you're sorting...in which case you presumably know what you're sorting. There are a whole host of tools to "deconvolve" mixed bulk RNA-seq samples into their relative proportions based on a single cell reference. CIBERSORTx is likely the most well-known among them, MuSiC is another option.

Results tend to be rather nonsense if your reference doesn't contain all the major cell types in your test sample.

[dviraran]

If you are looking to deconvolve mixed RNA-seq data, you are welcome to try our new xCell 2.0, now on bioconductor: https://bioconductor.org/packages/release/bioc/html/xCell2.html