Pyrepseq: the immune repertoire analysis toolkit

Pyrepseq is scipy & seaborn for studying adaptive immunity: modular implementations of algorithms for fast analyses, and bespoke plotting functions for compelling visualizations.

Documentation

You can install pyrepseq using pip:

pip install pyrepseq

For API documentation see below:

• API Reference
  • Main module
    • IO
      • isvalidaa()
      • isvalidcdr3()
      • multimerge()
      • standardize_dataframe()
    • Stats
      • chao1()
      • chao2()
      • jaccard_index()
      • overlap()
      • overlap_coefficient()
      • pc()
      • pc_conditional()
      • pc_grouped_cross()
      • pc_joint()
      • pc_n()
      • powerlaw_mle_alpha()
      • powerlaw_sample()
      • stdpc()
      • stdpc_joint()
      • stdpc_n()
      • subsample()
      • var_chao1()
      • var_chao2()
      • varpc_n()
    • Distance
      • calculate_neighbor_numbers()
      • cdist()
      • downsample()
      • find_neighbor_pairs()
      • find_neighbor_pairs_index()
      • hamming_neighbors()
      • hierarchical_clustering()
      • isdist1()
      • levenshtein_neighbors()
      • load_pcDelta_background()
      • next_nearest_neighbors()
      • nndist_hamming()
      • pcDelta()
      • pcDelta_grouped()
      • pcDelta_grouped_cross()
      • pdist()
    • Nearest Neighbor
      • LookupDB
        • LookupDB.lookup()
      • SymdelDB
        • SymdelDB.lookup()
      • calculate_sceptrdist_sparse()
      • hash_based()
      • kdtree()
      • nearest_neighbor()
      • nearest_neighbor_sceptrdist()
      • nearest_neighbor_tcrdist()
      • symdel()
  • Plotting submodule
    • align_seqs()
    • density_scatter()
    • label_axes()
    • labels_to_colors_hls()
    • labels_to_colors_tableau()
    • rankfrequency()
    • seqlogos()
    • seqlogos_vj()
    • similarity_clustermap()
  • Metrics
    • General Metrics
      • Metric
        • Metric.calc_cdist_matrix()
        • Metric.calc_pdist_vector()
        • Metric.name
      • Levenshtein
      • WeightedLevenshtein
    • TCR Metrics
      • TcrMetric
        • TcrMetric.calc_cdist_matrix()
        • TcrMetric.calc_pdist_vector()
      • AlphaCdr3Levenshtein
      • BetaCdr3Levenshtein
      • Cdr3Levenshtein
      • AlphaCdrLevenshtein
      • BetaCdrLevenshtein
      • CdrLevenshtein
      • AlphaCdr3Tcrdist
      • BetaCdr3Tcrdist
      • Cdr3Tcrdist
      • AlphaTcrdist
      • BetaTcrdist
      • Tcrdist