Index

_

__init__() (dandelion.Dandelion method)

A

add_cell_prefix() (dandelion.Dandelion method) add_cell_suffix() (dandelion.Dandelion method) add_sequence_prefix() (dandelion.Dandelion method)

add_sequence_suffix() (dandelion.Dandelion method) assign_isotype() (in module dandelion.preprocessing) assign_isotypes() (in module dandelion.preprocessing) assigngenes_igblast() (in module dandelion.external.immcantation.changeo)

B

barplot() (in module dandelion.plotting)

bin_expression() (in module dandelion.tools)

C

calculate_threshold() (in module dandelion.external.immcantation.shazam) chatterjee_corr() (in module dandelion.tools) check_contigs() (in module dandelion.preprocessing) clone_centrality() (in module dandelion.tools) clone_degree() (in module dandelion.tools) clone_diversity() (in module dandelion.tools) clone_network() (in module dandelion.plotting) clone_overlap() (in module dandelion.plotting) (in module dandelion.tools)

clone_rarefaction() (in module dandelion.plotting) (in module dandelion.tools) clone_size() (in module dandelion.tools) concat() (in module dandelion.utilities) copy() (dandelion.Dandelion method) create_germlines() (in module dandelion.preprocessing) creategermlines() (in module dandelion.external.immcantation.changeo)

D

dandelion module Dandelion (class in dandelion) dandelion.external.immcantation.changeo module dandelion.external.immcantation.scoper module dandelion.external.immcantation.shazam module dandelion.external.immcantation.tigger module dandelion.external.scanpy module

dandelion.logging module dandelion.plotting module dandelion.preprocessing module dandelion.tools module dandelion.utilities module define_clones() (in module dandelion.tools)

E

extract_edge_weights() (in module dandelion.tools)

F

filter_contigs() (in module dandelion.preprocessing) find_clones() (in module dandelion.tools)

format_fasta() (in module dandelion.preprocessing) format_fastas() (in module dandelion.preprocessing) from_scirpy() (in module dandelion.utilities)

G

generate_network() (in module dandelion.tools)

H

hierarchical_clones() (in module dandelion.external.immcantation.scoper)

I

identical_clones() (in module dandelion.external.immcantation.scoper)

L

load_data() (in module dandelion.utilities)

M

makeblastdb() (in module dandelion.utilities) makedb_igblast() (in module dandelion.external.immcantation.changeo) module dandelion dandelion.external.immcantation.changeo dandelion.external.immcantation.scoper dandelion.external.immcantation.shazam dandelion.external.immcantation.tigger dandelion.external.scanpy dandelion.logging dandelion.plotting dandelion.preprocessing dandelion.tools dandelion.utilities

P

parsedb_heavy() (in module dandelion.external.immcantation.changeo) parsedb_light() (in module dandelion.external.immcantation.changeo) print_header() (in module dandelion.logging) print_versions() (in module dandelion.logging)

productive_ratio() (in module dandelion.plotting) (in module dandelion.tools) project_pseudotime_to_cell() (in module dandelion.tools) pseudobulk_gex() (in module dandelion.tools) pseudotime_transfer() (in module dandelion.tools)

Q

quantify_mutations() (in module dandelion.external.immcantation.shazam)

R

read_10x_airr() (in module dandelion.utilities) read_10x_vdj() (in module dandelion.utilities) read_airr() (in module dandelion.utilities) read_bd_airr() (in module dandelion.utilities) read_h5ddl() (in module dandelion.utilities)

read_parse_airr() (in module dandelion.utilities) read_pkl() (in module dandelion.utilities) reannotate_genes() (in module dandelion.preprocessing) reassign_alleles() (in module dandelion.preprocessing) recipe_scanpy_qc() (in module dandelion.external.scanpy) reset_ids() (dandelion.Dandelion method)

S

setup_vdj_pseudobulk() (in module dandelion.tools) simplify() (dandelion.Dandelion method) spectral_clones() (in module dandelion.external.immcantation.scoper)

spectratype() (in module dandelion.plotting) stackedbarplot() (in module dandelion.plotting) store_germline_reference() (dandelion.Dandelion method)

T

tigger_genotype() (in module dandelion.external.immcantation.tigger)

to_scirpy() (in module dandelion.utilities) transfer() (in module dandelion.tools)

U

update_metadata() (dandelion.Dandelion method)

update_plus() (dandelion.Dandelion method)

V

vdj_pseudobulk() (in module dandelion.tools)

vj_usage_pca() (in module dandelion.tools)

W

write() (dandelion.Dandelion method) write_10x() (dandelion.Dandelion method)

write_airr() (dandelion.Dandelion method) write_h5ddl() (dandelion.Dandelion method) write_pkl() (dandelion.Dandelion method)