Scripts used for analysis of Mouse ENCODE DNaseI data.
Atlas and developmental dynamics of mouse DNase I hypersensitive sites Charles E. Breeze, John Lazar, Tim Mercer, Jessica Halow, Ida Washington, Kristen Lee, Sean Ibarrientos, Andres Castillo, Fidencio Neri, Eric Haugen, Eric Rynes, Alex Reynolds, Daniel Bates, Morgan Diegel, Douglas Dunn, Rajinder Kaul, Richard Sandstrom, Wouter Meuleman, M.A. Bender, Mark Groudine, John A. Stamatoyannopoulos bioRxiv 2020.06.26.172718; doi: https://doi.org/10.1101/2020.06.26.172718
Package of python/bash scripts, which parse the raw DNaseI data produced for the mouse ENCODE project to create the required data matrices for further analysis/visualization. Code requires Python 2.7 with with scikit-learn, numpy, scipy, matplotlib, pandas installations.
Visualizations and related analysis for manuscript figures are contained in ipython notebooks found in the ipython directory.
Various metadata files for DNaseI experiments