mir package

Subpackages

• mir.basic package
  • Submodules
  • mir.basic.gene_usage module
    • Allele Handling
    • precompute_olga_gene_usage_probabilities()
    • get_gene_usage_from_olga_model()
    • GeneUsage
      • GeneUsage.strip_alleles
      • GeneUsage.from_repertoire()
      • GeneUsage.from_sample()
      • GeneUsage.from_list()
      • GeneUsage.from_dataframe()
      • GeneUsage.loci
      • GeneUsage.total()
      • GeneUsage.vj_usage()
      • GeneUsage.v_usage()
      • GeneUsage.j_usage()
      • GeneUsage.vj_fraction()
      • GeneUsage.v_fraction()
      • GeneUsage.j_fraction()
      • GeneUsage.usage_comparison()
      • GeneUsage.correction_factors()
    • zscore_to_sigmoid()
    • compute_batch_corrected_gene_usage()
    • marginalize_batch_corrected_gene_usage()
  • mir.basic.pgen module
  • mir.basic.token_tables module
  • mir.basic.token_tables_pl module
    • Functions
    • expand_kmers()
    • summarize_by_gene()
    • summarize_by_gene_chunked()
    • summarize_by_pos()
    • summarize_by_pos_chunked()
    • summarize_by_v()
    • summarize_by_v_chunked()
    • summarize_by_c()
    • summarize_by_c_chunked()
    • fetch_by_kmer()
    • fetch_by_annotated_kmer()
  • mir.basic.tokens module
  • mir.basic.alphabets module
    • Types
    • Helpers
    • Alphabets
    • Translation
    • make_alphabet()
    • aa_to_reduced()
    • validate()
    • mask()
    • matches()
    • back_translate()
    • matches_aa_reduced()
  • mir.basic.aliases module
    • normalize_species_alias()
    • normalize_locus_alias()
    • normalize_airr_locus_value()
    • airr_aliases_for_locus()
    • locus_search_tokens()
  • mir.basic.mirseq_compat module
• mir.biomarkers package
  • Practical notes
    • ALICE vs TCRNET
    • Sequence logos and motif selection logos
  • Submodules
  • mir.biomarkers.motif_logo module
  • mir.biomarkers.token_stats module
  • mir.biomarkers.tcrnet module
  • mir.biomarkers.alice module
  • mir.biomarkers.gliph module
  • mir.biomarkers.metaclonotype_cluster module
• mir.common package
  • Submodules
  • mir.common.clonotype module
  • mir.common.diversity module
  • mir.common.filter module
  • mir.common.alleles module
  • mir.common.gene_library module
  • mir.common.parser module
  • mir.common.repertoire module
  • mir.common.metaclonotype module
  • mir.common.single_cell module
  • mir.common.single_cell_parser module
  • mir.common.single_cell_repair module
  • mir.common.single_cell_util module
  • mir.common.sampling module
  • mir.common.pool module
  • mir.common.control module
  • mir.common.io_parallel module
    • Parallel Default And Fallback Policy
  • mir.common.repertoire_dataset module
    • TSV And Parquet I/O Layouts
  • Module contents
• mir.comparative package
  • Submodules
  • mir.comparative.overlap module
  • mir.comparative.vdjbet module
  • mir.comparative.vdjbet_workflow module
• mir.distances package
  • Submodules
  • mir.distances.aligner module
  • mir.distances.seqdist module
  • mir.distances.tcrdist module
• mir.embedding package
  • Submodules
  • mir.embedding.bag_of_kmers module
  • mir.embedding.prototypes module
  • mir.embedding.tcremp module
• mir.graph package
  • Search behavior
  • Submodules
  • mir.graph.distance_utils module
  • mir.graph.edit_distance_graph module
  • mir.graph.neighborhood_enrichment module
  • mir.graph.token_graph module
  • mir.graph.single_cell_pairing module
  • Module contents
• mir.ml package
• mir.utils package
  • Submodules
  • mir.utils.embedding_diagnostics module
  • mir.utils.stats module
  • mir.utils.notebook_assets module
  • mir.utils.memory_debug module
  • mir.utils.shared_memory module
  • mir.utils.metaclonotype_clustering module
  • mir.utils.parser_cli module

Module contents

MIR library in python

mir.get_resource_path(name=None)