Welcome to hicberg’s documentation!

Contents:

• hicberg
  • hicberg package

Tutorial:

• Hicberg tutorial
  • Importing libraries
  • Paths and parameters setting
  • Step 0: Creating analyses directories
  • Step 1: Get chromosomes size and align reads
  • Step 3: Classification of read pairs
  • Step 4: Build contact matrix
  • Step 5: Profiling Hi-C data
  • Step 6: Infer ambiguous read pairs from statistical profile
  • Step 7: Build contact matrix with inferred read pairs
  • Step 8: Plot the reconstructed matrix and profiles
  • Step 9: Clean temppoary files

Indices and tables

• Index

• Module Index

• Search Page

hicberg

• hicberg package
  • Submodules
  • hicberg.align module
    • hic_align()
    • hic_build_index()
    • hic_index()
    • hic_sort()
    • hic_view()
  • hicberg.benchmark module
    • benchmark()
  • hicberg.eval module
    • arange_multi()
    • check_emptiness()
    • choice()
    • chromosight_cmd_generator()
    • draw_intervals()
    • generate_dict_coordinates()
    • get_FN_table()
    • get_FP_table()
    • get_TP_table()
    • get_bin_indexes()
    • get_boundaries()
    • get_chromosomes_intervals()
    • get_f1_score()
    • get_interval_index()
    • get_intervals_proportions()
    • get_precision()
    • get_recall()
    • get_top_pattern()
    • hicberg_benchmark_cmd_generator()
    • intersect2D()
    • overlap_intervals()
    • overlap_intervals_outer()
    • select_reads()
    • select_reads_multithreads()
    • select_reads_multithreads_bckp()
  • hicberg.io module
    • build_matrix()
    • build_pairs()
    • create_folder()
    • load_cooler()
    • load_dictionary()
    • merge_predictions()
    • tidy_folder()
  • hicberg.omics module
    • bedgraph_to_bigwig()
    • format_chrom_sizes()
    • get_bed_coverage()
    • get_bedgraph()
    • preprocess_pairs()
  • hicberg.pipeline module
    • check_tool()
    • pipeline()
  • hicberg.plot module
    • plot_benchmark()
    • plot_couple_repartition()
    • plot_coverages()
    • plot_d1d2()
    • plot_density()
    • plot_laws()
    • plot_matrix()
    • plot_pattern_reconstruction()
    • plot_trans_ps()
  • hicberg.statistics module
    • attribute_xs()
    • choice()
    • compute_density()
    • compute_propensity()
    • draw_read_couple()
    • generate_coverages()
    • generate_d1d2()
    • generate_density_map()
    • generate_density_map_backup()
    • generate_trans_ps()
    • generate_xs()
    • get_d1d2()
    • get_density()
    • get_dist_frags()
    • get_pair_cover()
    • get_pair_ps()
    • get_patterns()
    • get_restriction_map()
    • get_top_pattern()
    • get_trans_ps()
    • log_bin_genome()
    • pearson_score()
    • reattribute_reads()
  • hicberg.utils module
    • bam_iterator()
    • block_counter()
    • choice()
    • chunk_bam()
    • classify_reads()
    • detrend_matrix()
    • format_blacklist()
    • generate_gaussian_kernel()
    • get_bad_bins()
    • get_bin_table()
    • get_chromosomes_sizes()
    • get_chunks()
    • get_cis_distance()
    • get_local_density()
    • get_ordered_reads()
    • is_blacklisted()
    • is_circle()
    • is_duplicated()
    • is_empty_alignment()
    • is_intra_chromosome()
    • is_poor_quality()
    • is_reverse()
    • is_uncut()
    • is_unmapped()
    • is_unqualitative()
    • is_weird()
    • mad_smoothing()
    • max_consecutive_nans()
    • nan_conv()
    • replace_consecutive_zeros_with_mean()
    • subsample_restriction_map()
    • sum_mat_bins()
  • hicberg.version module
  • Module contents