metadensity

• metadensity package
  • Submodules
  • metadensity.config module
    • MetadensityConfig
      • MetadensityConfig.__init__()
      • MetadensityConfig.from_config_file()
  • metadensity.kmer_from_read module
    • get_all_site_seq()
    • main()
  • metadensity.metadensity module
    • Build_many_metagene()
    • Meta
      • Meta.__init__()
      • Meta.apply()
      • Meta.build_metagene()
      • Meta.concat_density_array()
      • Meta.convolve()
      • Meta.get_density_array()
      • Meta.get_feature_density_array()
      • Meta.save_deepdish()
      • Meta.scale_density_array()
    • Metadensity
      • Metadensity.__init__()
      • Metadensity.get_metadensity()
    • Metagene
      • Metagene.__init__()
      • Metagene.concat_density()
      • Metagene.concat_multi_feature()
      • Metagene.coverage_value()
      • Metagene.create_downstream_feature()
      • Metagene.create_feature()
      • Metagene.create_upstream_feature()
      • Metagene.from_dict()
      • Metagene.get_average_feature()
      • Metagene.get_raw_value()
      • Metagene.get_value()
      • Metagene.multi_feature_avg()
      • Metagene.order_multi_feature()
      • Metagene.remove_background()
      • Metagene.to_relative_axis()
      • Metagene.truncation_count()
      • Metagene.window_feature()
    • Metagene.self.featnames
    • Metagene.self.coverage
    • Metagene.self.sites
    • Metagene.self.value
    • Metagene.self.densities
    • Metagene.self.truncations
    • Metatruncate
      • Metatruncate.__init__()
      • Metatruncate.get_truncation()
    • Protein_coding_gene
      • Protein_coding_gene.__init__()
      • Protein_coding_gene.build_full_cds()
    • Protein_coding_gene.self.featnames
    • Protein_coding_gene.self.coverage
    • Protein_coding_gene.self.sites
    • Protein_coding_gene.self.value
    • Protein_coding_gene.self.densities
    • Protein_coding_gene.self.truncations
    • RNU
      • RNU.__init__()
    • RNU.self.featnames
    • RNU.self.coverage
    • RNU.self.sites
    • RNU.self.value
    • RNU.self.densities
    • RNU.self.truncations
    • STAMP
      • STAMP.__init__()
    • Window
      • Window.__init__()
    • YRNA
      • YRNA.__init__()
    • YRNA.self.featnames
    • YRNA.self.coverage
    • YRNA.self.sites
    • YRNA.self.value
    • YRNA.self.densities
    • YRNA.self.truncations
    • circRNA
      • circRNA.__init__()
    • circRNA.self.featnames
    • circRNA.self.coverage
    • circRNA.self.sites
    • circRNA.self.value
    • circRNA.self.densities
    • circRNA.self.truncations
    • density_array_entropy()
    • eCLIP
      • eCLIP.__init__()
      • eCLIP.calculate_coverage()
      • eCLIP.enough_coverage_transcript()
      • eCLIP.enough_transcripts()
      • eCLIP.find_idr_transcript()
      • eCLIP.from_series()
    • lncRNA
      • lncRNA.__init__()
    • lncRNA.self.featnames
    • lncRNA.self.coverage
    • lncRNA.self.sites
    • lncRNA.self.value
    • lncRNA.self.densities
    • lncRNA.self.truncations
    • miRNA
      • miRNA.__init__()
      • miRNA.find_hairpin()
    • miRNA.self.featnames
    • miRNA.self.coverage
    • miRNA.self.sites
    • miRNA.self.value
    • miRNA.self.densities
    • miRNA.self.truncations
    • nan_array()
    • rRNA
      • rRNA.__init__()
    • rRNA.self.featnames
    • rRNA.self.coverage
    • rRNA.self.sites
    • rRNA.self.value
    • rRNA.self.densities
    • rRNA.self.truncations
    • snoRNA
      • snoRNA.__init__()
    • snoRNA.self.featnames
    • snoRNA.self.coverage
    • snoRNA.self.sites
    • snoRNA.self.value
    • snoRNA.self.densities
    • snoRNA.self.truncations
    • tRNA
      • tRNA.__init__()
    • tRNA.self.featnames
    • tRNA.self.coverage
    • tRNA.self.sites
    • tRNA.self.value
    • tRNA.self.densities
    • tRNA.self.truncations
    • trim_or_pad()
    • vaultRNA
      • vaultRNA.__init__()
    • vaultRNA.self.featnames
    • vaultRNA.self.coverage
    • vaultRNA.self.sites
    • vaultRNA.self.value
    • vaultRNA.self.densities
    • vaultRNA.self.truncations
  • metadensity.plotd module
    • auto_rbp_color()
    • beautify()
    • calcaulte_grid_width()
    • generate_axis()
    • get_cmap()
    • get_xticklabels()
    • make_concat_xtick()
    • plot_enrich()
    • plot_mean_density()
    • plot_mean_density_concat()
    • plot_rbp_map()
    • rep_merge_options()
  • metadensity.pos_enrich module
    • KS_enrich()
    • PosEnrichResult
      • PosEnrichResult.__init__()
    • Wilcox_enrich()
    • auc_cum_dist()
    • auc_cum_wilcox()
    • construct_distribution()
    • enrich_by_thres()
    • mask_by_null()
    • null_thres()
  • metadensity.readdensity module
    • Density
      • Density.values()
    • Phastcon
      • Phastcon.__init__()
      • Phastcon.values()
    • ReadDensity
      • ReadDensity.__init__()
      • ReadDensity.pseudocount()
      • ReadDensity.rpm_to_r()
      • ReadDensity.total_mapped()
      • ReadDensity.values()
    • ReadDensity.self.neg
  • metadensity.region_call module
    • main()
    • nreads()
    • option_parser()
    • poission_pval()
    • region_based_calling()
  • metadensity.sequence module
    • count_kmer()
    • enrich_plot()
    • getRNAsequence()
    • get_interval_seq()
    • get_truncation_seq()
    • kmer()
    • kmer_rvalue()
    • kmer_zscore()
    • simulate_kmer_background()
  • metadensity.shape_from_read module
    • ks_all_pos()
    • many_intervals()
    • window_around()
    • window_around_eclip_sites()
    • windows_for_all()
  • metadensity.shrink_region module
    • Cluster
      • Cluster.__init__()
      • Cluster.enrich_score()
      • Cluster.make_fixed_size()
      • Cluster.to_bedstr()
    • control_cluster()
    • find_cluster()
    • get_cluster_seq()
    • main()
    • region_cluster()
    • region_cluster_ri()
  • metadensity.truncation module
    • fetch_reads()
    • get_mismatch()
    • read_start_sites()
    • strand_specific_pileup()
    • truncation_relative_axis()
  • Module contents