API Reference# Data loading and processing# arcfish.pp Data loading arcfish.pp.FOF_CT_Loader arcfish.pp.add_cell_type Preprocessing arcfish.pp.filter_normalize arcfish.pp.joint_filter_normalize arcfish.pp.median_pdist arcfish.pp.pseudo_count Tools# arcfish.tl Chromatin Loops General testing classes arcfish.tl.LoopTestAbstract arcfish.tl.TwoSampleT arcfish.tl.AxisWiseF Loop caller class arcfish.tl.LoopCaller Differential loop arcfish.tl.DiffLoop Other functions arcfish.tl.overlap arcfish.tl.signal_overlap arcfish.tl.loop_overlap arcfish.tl.all_possible_pairs TADs and Compartments TAD caller arcfish.tl.TADCaller Differential TADs arcfish.tl.DiffRegion A/B compartment caller arcfish.tl.ABCaller Wrapper Functions# arcfish.wr Tools Wrapper arcfish.wr.caller_wrapper Plotting modules# arcfish.pl arcfish.pl.cast_to_distmat arcfish.pl.pairwise_heatmap arcfish.pl.triangle_heatmap arcfish.pl.background_model arcfish.pl.compare_loops arcfish.pl.domain_boundary arcfish.pl.cpmt_bars