Implement Hidden-Markow-Models implemented in ChromstaR for genome-wide characterization of open chromatin landscape

[Temperche]

Hi everybody,

a nice feature would be to additionally have Hidden-Markow-Models as implemented in ChromstaR for genome-wide characterization of open chromatin landscape. The approach would be as described here: "On this approach control and stress condition were processed in two steps: (1) we fitted a univariate HMM over each ATAC-seq samples individually and (2) we performed a multivariate HMM over the combined ATAC-seq samples in each condition. For that, BAM files were processed under the differential mode, with a false discovery rate (FDR) cutoff of 0.05 and bin size of 500" Source: http://dx.doi.org/10.1101/824789

Again, thank you for your time!

Cheers
Temperche