New options for ChromHMM annotations or an option for the user to choose their own annotation

neurogenomics / EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

https://doi.org/doi:10.18129/B9.bioc.EpiCompare

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New options for ChromHMM annotations or an option for the user to choose their own annotation #119

Open teemuronkko opened 2 years ago

teemuronkko commented 2 years ago

I have been running EpiCompare on tip-seq data on oligodendrocytes and there seems to be no suitable ChromHMM annotation for these cells. Would it be possible to implement a way that the user can upload their own annotation file? If not, could more annotations be added to the chromHMM_annotation options?

josegarciamanteiga commented 1 year ago

I think that would be a perfect feature. Also because one can choose to download manually the chromHMM (or even produce them). The files then have to be split by 'name' and the mcols reorder a bit, but it can be done easily. For now it is in-built an hg19 to hg38 liftOver when you give one from the outside.