CHANGES IN VERSION 2.3.0 ------------------------ NEW FEATURES o Refactored the bootstrap approach to improve memory usage and reduce calculation time. o Added a plot_metagene function to produce a metagene plot from a data.frame to avoid always having to rely on the metagene object. o Deprecated the range and bin_size params. o Added new sections in the vignettes: "Managing large datasets" and "Comparing profiles with permutations". BUG FIXES o Removed params that no longer works with ggplot2 > 2.2.0. o Changed the seqlevels checks to match changes in GenomicAlignments. o Added a check to stop early and output clear error message when position in a GRanges is greater than the size of a chromosome. 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.