Pyrepseq: A Python library for analyzing immune repertoires

pyrepseq is a library that provides algorithms and visualization tools to speed up the analysis of immune repertoire sequencing data.

For now the package provides only limited functionality, though we envision that this will change in the future – contributions welcome!

Documentation

You can install pyrepseq using pip:

pip install pyrepseq

For API documentation see below:

• API Reference
  • main module
    • IO
      • isvalidaa()
      • isvalidcdr3()
      • multimerge()
    • Stats
      • jaccard_index()
      • overlap_coefficient()
      • powerlaw_mle_alpha()
      • powerlaw_sample()
    • 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()
  • plotting submodule
    • align_seqs()
    • label_axes()
    • labels_to_colors_hls()
    • labels_to_colors_tableau()
    • rankfrequency()
    • seqlogos()
    • seqlogos_vj()
    • similarity_clustermap()