Index

A

add_chain() (scirpy.io.IrCell method) AIRR Alellically included B-cells

AlignmentDistanceCalculator (class in scirpy.ir_dist) 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.AlignmentDistanceCalculator method) (scirpy.ir_dist.DistanceCalculator method) (scirpy.ir_dist.HammingDistanceCalculator method) (scirpy.ir_dist.IdentityDistanceCalculator method) (scirpy.ir_dist.LevenshteinDistanceCalculator method) (scirpy.ir_dist.ParallelDistanceCalculator method) CDR CDR3 cell_id() (scirpy.io.IrCell property) Chain locus chain_qc() (in module scirpy.tl)

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) DTYPE (scirpy.ir_dist.AlignmentDistanceCalculator attribute) (scirpy.ir_dist.DistanceCalculator attribute) (scirpy.ir_dist.HammingDistanceCalculator attribute) (scirpy.ir_dist.IdentityDistanceCalculator attribute) (scirpy.ir_dist.LevenshteinDistanceCalculator attribute) (scirpy.ir_dist.ParallelDistanceCalculator attribute)

Dual IR Dual TCR

E

embedding() (in module scirpy.pl)

Epitope

F

from_ir_objs() (in module scirpy.io)

G

group_abundance() (in module scirpy.pl) (in module scirpy.tl)

H

HammingDistanceCalculator (class in scirpy.ir_dist)

I

IdentityDistanceCalculator (class in scirpy.ir_dist) IG IR

ir_neighbors() (in module scirpy.pp) IrCell (class in scirpy.io) IrChain (class in scirpy.io)

L

layout_components() (in module scirpy.util.graph)

LevenshteinDistanceCalculator (class in scirpy.ir_dist) line() (in module scirpy.pl.base)

M

maynard2020() (in module scirpy.datasets) merge_with_ir() (in module scirpy.pp) module scirpy.datasets scirpy.io scirpy.ir_dist 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) 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.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) spectratype() (in module scirpy.pl) (in module scirpy.tl) style_axes() (in module scirpy.pl.styling) summarize_clonal_expansion() (in module scirpy.tl)

T

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

U

UMI

V

V(D)J VALID_LOCI (scirpy.io.IrChain attribute)

VDJ_LOCI (scirpy.io.IrChain attribute) vdj_usage() (in module scirpy.pl) VJ_LOCI (scirpy.io.IrChain attribute)

W

wu2020() (in module scirpy.datasets)

wu2020_3k() (in module scirpy.datasets)