Index A | B | C | D | E | F | G | H | I | K | L | M | O | P | R | S | T | U | V | W A adata (scirpy.util.DataHandler attribute) add_chain() (scirpy.io.AirrCell method) add_serialized_chains() (scirpy.io.AirrCell method) AIRR airr (scirpy.util.DataHandler attribute) airr() (in module scirpy.get) airr_context() (in module scirpy.get) AirrCell (class in scirpy.io) Alellically included B-cells AlignmentDistanceCalculator (class in scirpy.ir_dist.metrics) alpha_diversity() (in module scirpy.pl) (in module scirpy.tl) apply_style_to_axes() (in module scirpy.pl.styling) awkward array B bar() (in module scirpy.pl.base) barh() (in module scirpy.pl.base) BCR C calc_dist_mat() (scirpy.ir_dist.metrics.AlignmentDistanceCalculator method) (scirpy.ir_dist.metrics.DistanceCalculator method) (scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator method) (scirpy.ir_dist.metrics.HammingDistanceCalculator method) (scirpy.ir_dist.metrics.IdentityDistanceCalculator method) (scirpy.ir_dist.metrics.LevenshteinDistanceCalculator method) (scirpy.ir_dist.metrics.ParallelDistanceCalculator method) (scirpy.ir_dist.metrics.TCRdistDistanceCalculator method) CDR CDR3 cell_id (scirpy.io.AirrCell attribute) Chain locus chain_indices (scirpy.util.DataHandler attribute) chain_qc() (in module scirpy.tl) chains (scirpy.io.AirrCell attribute) check_schema_pre_v0_7() (scirpy.util.DataHandler static method) clear() (scirpy.io.AirrCell method) clonal_expansion() (in module scirpy.pl) (in module scirpy.tl) Clonotype Clonotype cluster Clonotype modularity clonotype_convergence() (in module scirpy.tl) clonotype_imbalance() (in module scirpy.pl) (in module scirpy.tl) clonotype_modularity() (in module scirpy.pl) (in module scirpy.tl) clonotype_network() (in module scirpy.pl) (in module scirpy.tl) clonotype_network_igraph() (in module scirpy.tl) Convergent evolution of clonotypes curve() (in module scirpy.pl.base) D data (scirpy.util.DataHandler attribute) DataHandler (class in scirpy.util) default() (scirpy.util.DataHandler static method) define_clonotype_clusters() (in module scirpy.tl) define_clonotypes() (in module scirpy.tl) DistanceCalculator (class in scirpy.ir_dist.metrics) DTYPE (scirpy.ir_dist.metrics.AlignmentDistanceCalculator attribute) (scirpy.ir_dist.metrics.DistanceCalculator attribute) (scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator attribute) (scirpy.ir_dist.metrics.HammingDistanceCalculator attribute) (scirpy.ir_dist.metrics.IdentityDistanceCalculator attribute) (scirpy.ir_dist.metrics.LevenshteinDistanceCalculator attribute) (scirpy.ir_dist.metrics.ParallelDistanceCalculator attribute) Dual IR Dual TCR E embedding() (in module scirpy.pl) empty_chain_dict() (scirpy.io.AirrCell static method) Epitope F FastAlignmentDistanceCalculator (class in scirpy.ir_dist.metrics) fields (scirpy.io.AirrCell attribute) from_airr_cells() (in module scirpy.io) from_dandelion() (in module scirpy.io) G get() (scirpy.io.AirrCell method) get_obs() (scirpy.util.DataHandler method) group_abundance() (in module scirpy.pl) (in module scirpy.tl) H HammingDistanceCalculator (class in scirpy.ir_dist.metrics) I IdentityDistanceCalculator (class in scirpy.ir_dist.metrics) iedb() (in module scirpy.datasets) IG igraph_from_sparse_matrix() (in module scirpy.util.graph) index_chains() (in module scirpy.pp) inject_param_docs() (scirpy.util.DataHandler static method) IR ir_dist() (in module scirpy.pp) ir_query() (in module scirpy.tl) ir_query_annotate() (in module scirpy.tl) ir_query_annotate_df() (in module scirpy.tl) items() (scirpy.io.AirrCell method) K keys() (scirpy.io.AirrCell method) L layout_components() (in module scirpy.util.graph) layout_fr_size_aware() (in module scirpy.util.graph) LevenshteinDistanceCalculator (class in scirpy.ir_dist.metrics) line() (in module scirpy.pl.base) M maynard2020() (in module scirpy.datasets) mdata (scirpy.util.DataHandler attribute) merge_airr() (in module scirpy.pp) module scirpy.datasets scirpy.get scirpy.io scirpy.ir_dist scirpy.pl scirpy.pp scirpy.tl scirpy.util Multi-tissue clonotype Multichain-cell O obs_context() (in module scirpy.get) Orphan chain P ParallelDistanceCalculator (class in scirpy.ir_dist.metrics) parasail_aa_alphabet (scirpy.ir_dist.metrics.TCRdistDistanceCalculator attribute) parasail_aa_alphabet_with_unknown (scirpy.ir_dist.metrics.TCRdistDistanceCalculator attribute) pop() (scirpy.io.AirrCell method) popitem() (scirpy.io.AirrCell method) Private clonotype Productive chain Public clonotype R read_10x_vdj() (in module scirpy.io) read_airr() (in module scirpy.io) read_bd_rhapsody() (in module scirpy.io) read_bracer() (in module scirpy.io) read_h5ad() (in module scirpy.io) read_h5mu() (in module scirpy.io) read_tracer() (in module scirpy.io) Receptor subtype Receptor type repertoire_overlap() (in module scirpy.pl) (in module scirpy.tl) S scirpy.datasets module scirpy.get module scirpy.io module scirpy.ir_dist module scirpy.pl module scirpy.pp module scirpy.tl module scirpy.util module sequence_dist() (in module scirpy.ir_dist) set_obs() (scirpy.util.DataHandler method) setdefault() (scirpy.io.AirrCell method) spectratype() (in module scirpy.pl) (in module scirpy.tl) squarify() (scirpy.ir_dist.metrics.AlignmentDistanceCalculator static method) (scirpy.ir_dist.metrics.DistanceCalculator static method) (scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator static method) (scirpy.ir_dist.metrics.HammingDistanceCalculator static method) (scirpy.ir_dist.metrics.IdentityDistanceCalculator static method) (scirpy.ir_dist.metrics.LevenshteinDistanceCalculator static method) (scirpy.ir_dist.metrics.ParallelDistanceCalculator static method) strings_to_categoricals() (scirpy.util.DataHandler method) style_axes() (in module scirpy.pl.styling) summarize_clonal_expansion() (in module scirpy.tl) T TCR tcr_dict_distance_matrix (scirpy.ir_dist.metrics.TCRdistDistanceCalculator attribute) tcr_nb_distance_matrix (scirpy.ir_dist.metrics.TCRdistDistanceCalculator attribute) TCRdistDistanceCalculator (class in scirpy.ir_dist.metrics) Tissue-specific clonotype to_airr_cells() (in module scirpy.io) to_airr_records() (scirpy.io.AirrCell method) to_dandelion() (in module scirpy.io) TYPE (scirpy.util.DataHandler attribute) U UMI update() (scirpy.io.AirrCell method) upgrade_schema() (in module scirpy.io) V V(D)J VALID_LOCI (scirpy.io.AirrCell attribute) values() (scirpy.io.AirrCell method) VDJ_LOCI (scirpy.io.AirrCell attribute) vdj_usage() (in module scirpy.pl) vdjdb() (in module scirpy.datasets) VJ_LOCI (scirpy.io.AirrCell attribute) W write_airr() (in module scirpy.io) wu2020() (in module scirpy.datasets) wu2020_3k() (in module scirpy.datasets)