lhe17
commented
2 years ago Hi,
Thank you for your question.
NEBULA is designed for single-cell RNA-seq data. I have not tried using it for spatial transcriptomics, so I’m not sure whether it will work in the context of spatial transcriptomics. Regarding the offset, the number of counts is more appropriate than the number of genes.
Best regards,
Liang
From: artemisiat @.> Sent: Thursday, April 21, 2022 4:58 PM To: lhe17/nebula @.> Cc: Subscribed @.***> Subject: [lhe17/nebula] Implementation on Spatial Transcriptomics (Issue #7)
Thanks for this package! I was wondering which variable you would recommend using as offset in the context of spatial transcriptomics. Every "cell" in this case includes on average 4-5 cells and I am unsure if number of counts or genes would be more appropriate. Thanks!
— Reply to this email directly, view it on GitHub https://github.com/lhe17/nebula/issues/7 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AGDISURV7IGP7NOSTVKZKGLVGG6OBANCNFSM5UAMXRWQ . You are receiving this because you are subscribed to this thread. https://github.com/notifications/beacon/AGDISUS6H4O3M36W4VQJ7PLVGG6OBA5CNFSM5UAMXRW2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4SBWW5WA.gif Message ID: @. @.> >
Thanks for this package! I was wondering which variable you would recommend using as offset in the context of spatial transcriptomics. Every "cell" in this case includes on average 4-5 cells and I am unsure if number of counts or genes would be more appropriate. Thanks!