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SONGDONGYUAN1994 / PseudotimeDE

A robust DE test method that accounts for the uncertainty in pseudotime inference
MIT License
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For bulk RNAseq #4

Closed hchetia closed 3 years ago

hchetia commented 3 years ago

Has this method been tested also for bulk-RNAseq data?

SONGDONGYUAN1994 commented 3 years ago

Hi, This method hasn't been tested for bulk-RNAseq data. Based on my knowledge, people do not use pseudotime in bulk-RNA-seq (if I am wrong, please tell me!) Of course, you can try the "fix" mode if your data is time-course data. However, please notice that a GAM needs many time points due to its high model degree of freedom (perhaps more than 10 time points). If you only have a few time points the method will not work. Thanks!

hchetia commented 3 years ago

Hi @SONGDONGYUAN1994 Thanks for the reply. Literature shows that Phenopath by Kieran Campbell is one of the tools that can allow pseudotime based inference from bulk RNAseq data.