Index

A

add_chain() (scirpy.io.AirrCell method) add_serialized_chains() (scirpy.io.AirrCell method) AIRR 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)

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.HammingDistanceCalculator method) (scirpy.ir_dist.metrics.IdentityDistanceCalculator method) (scirpy.ir_dist.metrics.LevenshteinDistanceCalculator method) (scirpy.ir_dist.metrics.ParallelDistanceCalculator method) CDR CDR3 cell_id() (scirpy.io.AirrCell property) Chain locus chain_qc() (in module scirpy.tl) chains() (scirpy.io.AirrCell property)

clear() (scirpy.io.AirrCell method) clonal_expansion() (in module scirpy.pl) (in module scirpy.tl) Clonotype Clonotype cluster clonotype_convergence() (in module scirpy.tl) clonotype_imbalance() (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

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.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

fields() (scirpy.io.AirrCell property)

from_airr_cells() (in module scirpy.io) from_dandelion() (in module scirpy.io)

G

get() (scirpy.io.AirrCell 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) IG igraph_from_sparse_matrix() (in module scirpy.util.graph)

IR ir_dist() (in module scirpy.pp) 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) merge_airr_chains() (in module scirpy.pp) merge_with_ir() (in module scirpy.pp) module scirpy.datasets scirpy.io scirpy.ir_dist scirpy.ir_dist.metrics scirpy.pl scirpy.pl.base scirpy.pl.styling scirpy.pp scirpy.tl scirpy.util

Multi-tissue clonotype Multichain-cell

O

Orphan chain

P

ParallelDistanceCalculator (class in scirpy.ir_dist.metrics) 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_bracer() (in module scirpy.io) read_h5ad() (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.io module scirpy.ir_dist module scirpy.ir_dist.metrics module scirpy.pl module scirpy.pl.base module scirpy.pl.styling module scirpy.pp module

scirpy.tl module scirpy.util module sequence_dist() (in module scirpy.ir_dist) 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.HammingDistanceCalculator static method) (scirpy.ir_dist.metrics.IdentityDistanceCalculator static method) (scirpy.ir_dist.metrics.LevenshteinDistanceCalculator static method) (scirpy.ir_dist.metrics.ParallelDistanceCalculator static method) style_axes() (in module scirpy.pl.styling) summarize_clonal_expansion() (in module scirpy.tl)

T

TCR Tissue-specific clonotype to_airr_cells() (in module scirpy.io)

to_airr_records() (scirpy.io.AirrCell method) to_dandelion() (in module scirpy.io) to_scirpy_record() (scirpy.io.AirrCell method)

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) VJ_LOCI (scirpy.io.AirrCell attribute)

W

write_airr() (in module scirpy.io)

wu2020() (in module scirpy.datasets) wu2020_3k() (in module scirpy.datasets)