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theislab / diffxpy

Differential expression analysis for single-cell RNA-seq data.
https://diffxpy.rtfd.io
BSD 3-Clause "New" or "Revised" License
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Bulk RNAseq #150

Closed wangjiawen2013 closed 4 years ago

wangjiawen2013 commented 4 years ago

Can diffxpy be used to analysis differential expression of bulk RNAseq data? just like edgeR and DESeq2.

davidsebfischer commented 4 years ago

Hi @wangjiawen2013! Yes, you can do that! Notice though that we do not have empirical Bayes on dispersion estiamtes implemented, so you might overfits dispersion, DESeq2 is nice in that case! We are working on empirical Bayes but it is not very high up the list as it is not standardly used in single-cell, where you have many more observations.