CHANGES FOR VERSION 2.2.0 ------------------------ o Added checks to avoid producing identical matrices or data frame when the parameters are still the same after first function call. o Splitted the analysis in multiple (optionnal) intermediate steps (add_design, produce_matrices and produce_data_frame). o narrowPeak and broadPeak format is now supported. o Added multiple getter to access metagene members that are all now private (get_params, get_design, get_regions, get_matrices, get_data_frame, get_plot, get_raw_coverages and get_normalized_coverages. o Added the NCIS algorithm for noise removal. o Replaced the old datasets with promoters_hg19, promoters_hg18, promoters_mm10 and promoters_mm9 that can be accessed with data(promoters_????). o Added flip_regions and unflip_regions to switch regions orientation based on the strand.