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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
193 stars 23 forks source link

Marker Gene Identification #162

Open HypoChloremic opened 4 years ago

HypoChloremic commented 4 years ago

Hello, diffxpy has been recommended as being a go to for performing differential gene expression analysis in the scanpy project. However, the documentation for intention of use is lacking. For instance, when performing marker gene identification, there is no documentation for it in diffxpy.

Thus far I have resorted to the following: 

adata.obs['tmp'] = [ '0' if i == cl else '1' for i in adata.obs[clusterColumn]
rank = de.test.t_test( data = adata, grouping = 'tmp' )

I.e. separate cluster of interest from the rest, thereafter perform a differential gene expression.

Is this sufficent for marker identification in diffxpy, @falexwolf, @davidsebfischer ?

auesro commented 2 years ago

Came across this issue wondering exactly the same. Any answers?