andreaskapou/scmet

Bayesian modelling of DNA methylation heterogeneity at single-cell resolution

scmet's Issues

data conversion process

Do you have a video or a manual providing the data conversion process for gastrulation？

How can I apply scMET on real data? And does it do imputation?

Hello dear author, it's exciting to find this new tool!
I've been following Mellisa but gave up due to the lack of detailed annotation of genome features, could you please give a brief suggestion what's the difference of scMET and Melissa, and how to determine which tool is more suitable for my data?
Also, when I check "Online vignette", I found "scMET on real data: TODO", can I perform the same analysis according to the synthetic data tutorial?
Thanks!

Apply scMET on sliding windows

Hello Dear Andreas,

I was trying to apply scMET on a large-scale scBS-seq dataset using non-overlapping sliding windows of 20kb. I noticed that you has suggested in the scMET paper:

In the spirit of divide-and-conquer schemes, we bypass this problem via a parallelization strategy in which we apply scMET separately to each chromosome. Feature-specific estimates obtained for each chromosome can be combined post hoc when performing HVF selection and differential analyses.

Do you have any instructions on how to combine the estimates post hoc? Or any functions developed for that purpose? Thanks in advance! Looking forward to hearing you back.

Best,
Ning

How to use multiple CPU threads?

Hi there,
thanks for making this tool! I'm currently trying it out and noticed that scMET uses only a single core even when I set n_cores to a higher number. Is this a bug or do I have to register the threads first (if so, how)?
Cheers, Lukas