Index _ | A | B | C | D | E | F | G | I | J | L | M | N | O | P | R | S | T | W _ __init__() (arcfish.pp.FOF_CT_Loader method) (arcfish.tl.ABCaller method) (arcfish.tl.AxisWiseF method) (arcfish.tl.DiffLoop method) (arcfish.tl.DiffRegion method) (arcfish.tl.LoopCaller method) (arcfish.tl.LoopTestAbstract method) (arcfish.tl.TADCaller method) (arcfish.tl.TwoSampleT method) A ABCaller (class in arcfish.tl) add_cell_type() (in module arcfish.pp) all_possible_pairs() (in module arcfish.tl) append_pval() (arcfish.tl.AxisWiseF method) (arcfish.tl.LoopTestAbstract method) (arcfish.tl.TwoSampleT method) append_summit() (arcfish.tl.AxisWiseF method) (arcfish.tl.LoopTestAbstract method) (arcfish.tl.TwoSampleT method) AxisWiseF (class in arcfish.tl) B background_model() (in module arcfish.pl) by_axes_pc() (arcfish.tl.ABCaller method) by_first_pc() (arcfish.tl.ABCaller method) by_insulation() (arcfish.tl.TADCaller method) by_pval() (arcfish.tl.TADCaller method) C call_cpmt() (arcfish.tl.ABCaller method) call_loops() (arcfish.tl.LoopCaller method) call_tads() (arcfish.tl.TADCaller method) caller_wrapper() (in module arcfish.wr) cast_to_distmat() (in module arcfish.pl) chr_ids (arcfish.pp.FOF_CT_Loader property) compare_loops() (in module arcfish.pl) cpmt_bars() (in module arcfish.pl) create_adata() (arcfish.pp.FOF_CT_Loader method) D diff_loops() (arcfish.tl.DiffLoop method) diff_region() (arcfish.tl.DiffRegion method) DiffLoop (class in arcfish.tl) DiffRegion (class in arcfish.tl) distance (arcfish.tl.TADCaller property) domain_boundary() (in module arcfish.pl) E entry_pvals() (arcfish.tl.DiffLoop static method) F fdr_cutoff (arcfish.tl.LoopCaller property) (arcfish.tl.TADCaller property) filter_normalize() (in module arcfish.pp) FOF_CT_Loader (class in arcfish.pp) G gap (arcfish.tl.LoopCaller property) I ij_background() (arcfish.tl.AxisWiseF static method) (arcfish.tl.LoopTestAbstract static method) (arcfish.tl.TwoSampleT static method) info (arcfish.pp.FOF_CT_Loader property) J joint_filter_normalize() (in module arcfish.pp) L loop_overlap() (in module arcfish.tl) loop_pvals() (arcfish.tl.DiffLoop static method) loop_range (arcfish.tl.LoopCaller property) LoopCaller (class in arcfish.tl) LoopTestAbstract (class in arcfish.tl) M median_pdist() (in module arcfish.pp) method (arcfish.tl.TADCaller property) min_tad_size (arcfish.tl.TADCaller property) N nm_ratio (arcfish.pp.FOF_CT_Loader property) O outer_cut (arcfish.tl.LoopCaller property) overlap() (in module arcfish.tl) P pairwise_heatmap() (in module arcfish.pl) path (arcfish.pp.FOF_CT_Loader property) prominence (arcfish.tl.TADCaller property) pseudo_count() (in module arcfish.pp) pval_cutoff (arcfish.tl.LoopCaller property) pval_to_fdr() (arcfish.tl.DiffLoop static method) R read_data() (arcfish.pp.FOF_CT_Loader method) region_pvals() (arcfish.tl.DiffRegion static method) S signal_overlap() (in module arcfish.tl) spread_label() (arcfish.tl.LoopCaller method) T TADCaller (class in arcfish.tl) to_bedpe() (arcfish.tl.DiffLoop method) (arcfish.tl.DiffRegion method) (arcfish.tl.LoopCaller method) (arcfish.tl.TADCaller method) tree (arcfish.tl.TADCaller property) triangle_heatmap() (in module arcfish.pl) tss (arcfish.tl.ABCaller property) TwoSampleT (class in arcfish.tl) W window (arcfish.tl.TADCaller property)