Index

A

arange_multi() (in module hicberg.eval)

attribute_xs() (in module hicberg.statistics)

B

bam_iterator() (in module hicberg.utils) bedgraph_to_bigwig() (in module hicberg.omics) benchmark() (in module hicberg.benchmark)

block_counter() (in module hicberg.utils) build_matrix() (in module hicberg.io) build_pairs() (in module hicberg.io)

C

check_emptiness() (in module hicberg.eval) check_tool() (in module hicberg.pipeline) choice() (in module hicberg.eval) (in module hicberg.statistics) (in module hicberg.utils)

chromosight_cmd_generator() (in module hicberg.eval) chunk_bam() (in module hicberg.utils) classify_reads() (in module hicberg.utils) compute_density() (in module hicberg.statistics) compute_propensity() (in module hicberg.statistics) create_folder() (in module hicberg.io)

D

detrend_matrix() (in module hicberg.utils)

draw_intervals() (in module hicberg.eval) draw_read_couple() (in module hicberg.statistics)

F

format_blacklist() (in module hicberg.utils)

format_chrom_sizes() (in module hicberg.omics)

G

generate_coverages() (in module hicberg.statistics) generate_d1d2() (in module hicberg.statistics) generate_density_map() (in module hicberg.statistics) generate_density_map_backup() (in module hicberg.statistics) generate_dict_coordinates() (in module hicberg.eval) generate_gaussian_kernel() (in module hicberg.utils) generate_trans_ps() (in module hicberg.statistics) generate_xs() (in module hicberg.statistics) get_bad_bins() (in module hicberg.utils) get_bed_coverage() (in module hicberg.omics) get_bedgraph() (in module hicberg.omics) get_bin_indexes() (in module hicberg.eval) get_bin_table() (in module hicberg.utils) get_boundaries() (in module hicberg.eval) get_chromosomes_intervals() (in module hicberg.eval) get_chromosomes_sizes() (in module hicberg.utils) get_chunks() (in module hicberg.utils) get_cis_distance() (in module hicberg.utils) get_d1d2() (in module hicberg.statistics)

get_density() (in module hicberg.statistics) get_dist_frags() (in module hicberg.statistics) get_f1_score() (in module hicberg.eval) get_FN_table() (in module hicberg.eval) get_FP_table() (in module hicberg.eval) get_interval_index() (in module hicberg.eval) get_intervals_proportions() (in module hicberg.eval) get_local_density() (in module hicberg.utils) get_ordered_reads() (in module hicberg.utils) get_pair_cover() (in module hicberg.statistics) get_pair_ps() (in module hicberg.statistics) get_patterns() (in module hicberg.statistics) get_precision() (in module hicberg.eval) get_recall() (in module hicberg.eval) get_restriction_map() (in module hicberg.statistics) get_top_pattern() (in module hicberg.eval) (in module hicberg.statistics) get_TP_table() (in module hicberg.eval) get_trans_ps() (in module hicberg.statistics)

H

hic_align() (in module hicberg.align) hic_build_index() (in module hicberg.align) hic_index() (in module hicberg.align) hic_sort() (in module hicberg.align) hic_view() (in module hicberg.align) hicberg module hicberg.align module hicberg.benchmark module hicberg.eval module hicberg.io module

hicberg.omics module hicberg.pipeline module hicberg.plot module hicberg.statistics module hicberg.utils module hicberg.version module hicberg_benchmark_cmd_generator() (in module hicberg.eval)

I

intersect2D() (in module hicberg.eval) is_blacklisted() (in module hicberg.utils) is_circle() (in module hicberg.utils) is_duplicated() (in module hicberg.utils) is_empty_alignment() (in module hicberg.utils) is_intra_chromosome() (in module hicberg.utils)

is_poor_quality() (in module hicberg.utils) is_reverse() (in module hicberg.utils) is_uncut() (in module hicberg.utils) is_unmapped() (in module hicberg.utils) is_unqualitative() (in module hicberg.utils) is_weird() (in module hicberg.utils)

L

load_cooler() (in module hicberg.io)

load_dictionary() (in module hicberg.io) log_bin_genome() (in module hicberg.statistics)

M

mad_smoothing() (in module hicberg.utils) max_consecutive_nans() (in module hicberg.utils) merge_predictions() (in module hicberg.io) module hicberg hicberg.align hicberg.benchmark hicberg.eval hicberg.io hicberg.omics hicberg.pipeline hicberg.plot hicberg.statistics hicberg.utils hicberg.version

N

nan_conv() (in module hicberg.utils)

O

overlap_intervals() (in module hicberg.eval)

overlap_intervals_outer() (in module hicberg.eval)

P

pearson_score() (in module hicberg.statistics) pipeline() (in module hicberg.pipeline) plot_benchmark() (in module hicberg.plot) plot_couple_repartition() (in module hicberg.plot) plot_coverages() (in module hicberg.plot) plot_d1d2() (in module hicberg.plot)

plot_density() (in module hicberg.plot) plot_laws() (in module hicberg.plot) plot_matrix() (in module hicberg.plot) plot_pattern_reconstruction() (in module hicberg.plot) plot_trans_ps() (in module hicberg.plot) preprocess_pairs() (in module hicberg.omics)

R

reattribute_reads() (in module hicberg.statistics)

replace_consecutive_zeros_with_mean() (in module hicberg.utils)

S

select_reads() (in module hicberg.eval) select_reads_multithreads() (in module hicberg.eval)

select_reads_multithreads_bckp() (in module hicberg.eval) subsample_restriction_map() (in module hicberg.utils) sum_mat_bins() (in module hicberg.utils)

T

tidy_folder() (in module hicberg.io)