omicsdata package

Subpackages

• omicsdata.npz package
  • Submodules
  • omicsdata.npz.archive module
    • Archive
      • Archive.add()
      • Archive.get()
      • Archive.get_mutrel()
      • Archive.has()
      • Archive.save()
  • Module contents
• omicsdata.ssm package
  • Submodules
  • omicsdata.ssm.columns module
    • PARAMS_Columns
      • PARAMS_Columns.CLUSTERS
      • PARAMS_Columns.GARBAGE
      • PARAMS_Columns.SAMPLES
    • SSM_Columns
      • SSM_Columns.COL_ORDER
      • SSM_Columns.ID
      • SSM_Columns.NAME
      • SSM_Columns.TOTAL_READS
      • SSM_Columns.VAR_READS
      • SSM_Columns.VAR_READ_PROB
  • omicsdata.ssm.common module
    • extract_vids()
    • sort_vids()
  • omicsdata.ssm.constants module
    • Variants_Keys
      • Variants_Keys.CHROM
      • Variants_Keys.ID
      • Variants_Keys.NAME
      • Variants_Keys.OMEGA_V
      • Variants_Keys.POS
      • Variants_Keys.REF_READS
      • Variants_Keys.TOTAL_READS
      • Variants_Keys.VAF
      • Variants_Keys.VAR_READS
  • omicsdata.ssm.convert module
    • ssm_to_pyclone()
    • ssm_to_viber()
  • omicsdata.ssm.parse module
    • extract_nums()
    • load_params()
    • load_ssm()
    • load_ssms_and_params()
    • remove_garbage()
    • write_params()
    • write_ssms()
  • omicsdata.ssm.supervariants module
    • Variant
      • Variant.id
      • Variant.omega_v
      • Variant.ref_reads
      • Variant.total_reads
      • Variant.vaf
      • Variant.var_reads
    • clusters_to_supervars()
    • convert_all_variants_to_tuples()
    • convert_variant_dict_to_tuple()
    • make_superclusters()
    • make_supervar()
    • supervars_to_binom_params()
  • Module contents
• omicsdata.tree package
  • Submodules
  • omicsdata.tree.adj module
    • adj_to_anc()
    • adj_to_parents()
  • omicsdata.tree.columns module
    • NEUTREE_Columns
      • NEUTREE_Columns.CLUSTERINGS
      • NEUTREE_Columns.COUNTS
      • NEUTREE_Columns.GARBAGE
      • NEUTREE_Columns.LOGSCORES
      • NEUTREE_Columns.PHIS
      • NEUTREE_Columns.STRUCTS
  • omicsdata.tree.parents module
    • compute_partial_parents()
    • parents_to_adj()
  • omicsdata.tree.neutree module
    • Neutree
      • Neutree.clusterings
      • Neutree.counts
      • Neutree.garbage
      • Neutree.logscores
      • Neutree.phis
      • Neutree.structs
    • load()
    • save()
  • Module contents

Module contents