Preparation steps:

  1. made a universe of regions by merging regions across cell types defined as opened in ENCODE

  2. took bigwig files from ENCODE for individual cell types, merged replicates, filtered out blacklisted sites

  3. evaluated the signal above regions defined by previous step

  4. performed quantile normalization

  5. subsetted it



data.frame, rows represent whole selection of open chromatin regions across all cell types defined by ENCODE, columns are individual cell types and values are normalized open chromatin signal values.