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Adding the new captured Hi-C module. Viewpoint analysis based on a background model, significant interaction detection and differential analysis are provided. Thanks to @rgilsbach and @DonStephano .
Adding documentation for captured Hi-C module and a tutorial on how to use it.
Adding a module to be able to detect quite fast the quality of a Hi-C data set: hicQuickQC.
Adding a tool to merge loops of different resolutions.
Improving validation of locations: Presorting is no longer necessary; adding feature to add 'chr' prefix to loop or protein chromosome name
Change loop detection slightly to improve results and fixed bugs:
preselection p-value was ignored and only p-value was used
adding additional test to the peak region test to decrease false discoveries
exchanging pThreshold / ln(distance) to remove too low values by a share of the maximum value of the distance. New parameter 'maximumInteractionPercentageThreshold'
Removal of the folder 'scripts' and its content. These were outdated scripts and will maybe part of regular Hi-C tools in the future.