Index

A

add_chain() (scirpy.io.TcrCell method) AlignmentDistanceCalculator (class in scirpy.tcr_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)

C

calc_dist_mat() (scirpy.tcr_dist.AlignmentDistanceCalculator method) (scirpy.tcr_dist.DistanceCalculator method) (scirpy.tcr_dist.IdentityDistanceCalculator method) (scirpy.tcr_dist.LevenshteinDistanceCalculator method) (scirpy.tcr_dist.ParallelDistanceCalculator method) CDR CDR3 cell_id() (scirpy.io.TcrCell property) chain_pairing() (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.tcr_dist) DTYPE (scirpy.tcr_dist.AlignmentDistanceCalculator attribute) (scirpy.tcr_dist.DistanceCalculator attribute) (scirpy.tcr_dist.IdentityDistanceCalculator attribute) (scirpy.tcr_dist.LevenshteinDistanceCalculator attribute) (scirpy.tcr_dist.ParallelDistanceCalculator attribute)

Dual TCR

E

embedding() (in module scirpy.pl)

Epitope

F

from_tcr_objs() (in module scirpy.io)

G

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

I

IdentityDistanceCalculator (class in scirpy.tcr_dist)

L

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

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

M

merge_with_tcr() (in module scirpy.pp) module scirpy.datasets scirpy.io scirpy.pl scirpy.pl.base scirpy.pl.styling scirpy.pp scirpy.tcr_dist scirpy.tl scirpy.util

Multi-tissue clonotype Multichain-cell

O

Orphan chain

P

ParallelDistanceCalculator (class in scirpy.tcr_dist) Private clonotype

productive chain Public clonotype

R

read_10x_vdj() (in module scirpy.io) read_airr() (in module scirpy.io) read_h5ad() (in module scirpy.io)

read_tracer() (in module scirpy.io) repertoire_overlap() (in module scirpy.pl) (in module scirpy.tl)

S

scirpy.datasets module scirpy.io module scirpy.pl module scirpy.pl.base module scirpy.pl.styling module scirpy.pp module

scirpy.tcr_dist module scirpy.tl module scirpy.util module 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 tcr_dist() (in module scirpy.tcr_dist) tcr_neighbors() (in module scirpy.pp)

TcrCell (class in scirpy.io) TcrChain (class in scirpy.io) Tissue-specific clonotype

U

UMI

V

V(D)J

vdj_usage() (in module scirpy.pl)

W

wu2020() (in module scirpy.datasets)

wu2020_3k() (in module scirpy.datasets)