Index

A

add_cell_prefix() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) add_cell_suffix() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) add_sequence_prefix() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) add_sequence_suffix() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

assign_isotype() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) assign_isotypes() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) assigngenes_igblast() (in module dandelion.external.immcantation.base.changeo) (in module dandelion.external.immcantation.polars.changeo)

B

barplot() (in module dandelion.base.plotting) (in module dandelion.polars.plotting)

C

calculate_threshold() (in module dandelion.external.immcantation.base.shazam) (in module dandelion.external.immcantation.polars.shazam) check_contigs() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) clone() (dandelion.polars.core.Dandelion method) clone_centrality() (in module dandelion.base.tools) (in module dandelion.polars.tools) clone_circlepackplot() (in module dandelion.base.plotting) (in module dandelion.polars.plotting) clone_degree() (in module dandelion.base.tools) (in module dandelion.polars.tools) clone_diversity() (in module dandelion.base.tools) (in module dandelion.polars.tools) clone_network() (in module dandelion.base.plotting) (in module dandelion.polars.plotting) clone_overlap() (in module dandelion.base.plotting) (in module dandelion.base.tools) (in module dandelion.polars.plotting) (in module dandelion.polars.tools)

clone_rarefaction() (in module dandelion.base.tools) (in module dandelion.polars.tools) clone_size() (in module dandelion.base.tools) (in module dandelion.polars.tools) clone_view() (in module dandelion.base.tools) (in module dandelion.polars.tools) compute() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) concat() (in module dandelion.base.tools) (in module dandelion.polars.tools) copy() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) creategermlines() (in module dandelion.external.immcantation.base.changeo) (in module dandelion.external.immcantation.polars.changeo)

D

dandelion module dandelion.base.io module dandelion.base.plotting module dandelion.base.preprocessing module dandelion.base.tools module dandelion.external.immcantation.base.changeo module dandelion.external.immcantation.base.scoper module dandelion.external.immcantation.base.shazam module dandelion.external.immcantation.polars.changeo module dandelion.external.immcantation.polars.scoper module dandelion.external.immcantation.polars.shazam module dandelion.external.immcantation.tigger module

dandelion.external.scanpy module dandelion.logging module dandelion.polars.io module dandelion.polars.plotting module dandelion.polars.preprocessing module dandelion.polars.tools module dandelion.tutorial module dandelion.utilities module data (dandelion.base.core.Dandelion property) (dandelion.polars.core.Dandelion property) data_names (dandelion.base.core.Dandelion property) (dandelion.polars.core.Dandelion property) define_clones() (in module dandelion.base.tools) (in module dandelion.polars.tools)

E

extract_edge_weights() (in module dandelion.base.tools) (in module dandelion.polars.tools) (in module dandelion.utilities)

F

find_clones() (in module dandelion.base.tools) (in module dandelion.polars.tools) format_fasta() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing)

format_fastas() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) from_scirpy() (in module dandelion.base.tools) (in module dandelion.polars.tools)

G

generate_network() (in module dandelion.base.tools) (in module dandelion.polars.tools)

H

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

I

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

M

makeblastdb() (in module dandelion.utilities) makedb_igblast() (in module dandelion.external.immcantation.base.changeo) (in module dandelion.external.immcantation.polars.changeo) metadata (dandelion.base.core.Dandelion property) (dandelion.polars.core.Dandelion property) metadata_names (dandelion.base.core.Dandelion property) (dandelion.polars.core.Dandelion property) module dandelion dandelion.base.io dandelion.base.plotting dandelion.base.preprocessing dandelion.base.tools dandelion.external.immcantation.base.changeo dandelion.external.immcantation.base.scoper dandelion.external.immcantation.base.shazam dandelion.external.immcantation.polars.changeo dandelion.external.immcantation.polars.scoper dandelion.external.immcantation.polars.shazam dandelion.external.immcantation.tigger dandelion.external.scanpy dandelion.logging dandelion.polars.io dandelion.polars.plotting dandelion.polars.preprocessing dandelion.polars.tools dandelion.tutorial dandelion.utilities

N

n_contigs (dandelion.polars.core.Dandelion property)

n_obs (dandelion.polars.core.Dandelion property)

P

parsedb_heavy() (in module dandelion.external.immcantation.base.changeo) (in module dandelion.external.immcantation.polars.changeo) parsedb_light() (in module dandelion.external.immcantation.base.changeo) (in module dandelion.external.immcantation.polars.changeo) print_header() (in module dandelion.logging) print_versions() (in module dandelion.logging) productive_ratio() (in module dandelion.base.plotting) (in module dandelion.base.tools) (in module dandelion.polars.plotting) (in module dandelion.polars.tools)

project_pseudotime_to_cell() (in module dandelion.base.tools) (in module dandelion.polars.tools) pseudobulk_gex() (in module dandelion.base.tools) (in module dandelion.polars.tools) pseudotime_transfer() (in module dandelion.base.tools) (in module dandelion.polars.tools)

Q

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

R

read() (in module dandelion.base.io) (in module dandelion.polars.io) read_10x_airr() (in module dandelion.base.io) (in module dandelion.polars.io) read_10x_vdj() (in module dandelion.base.io) (in module dandelion.polars.io) read_airr() (in module dandelion.base.io) (in module dandelion.polars.io) read_bd_airr() (in module dandelion.base.io) (in module dandelion.polars.io) read_ddl() (in module dandelion.base.io) (in module dandelion.polars.io)

read_h5ddl() (in module dandelion.base.io) (in module dandelion.polars.io) read_parse_airr() (in module dandelion.base.io) (in module dandelion.polars.io) read_seekgene_vdj() (in module dandelion.base.io) (in module dandelion.polars.io) read_zipddl() (in module dandelion.polars.io) reannotate_genes() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) reassign_alleles() (in module dandelion.base.preprocessing) (in module dandelion.polars.preprocessing) recipe_scanpy_qc() (in module dandelion.external.scanpy) reset_ids() (dandelion.polars.core.Dandelion method)

S

set_backend() (in module dandelion) setup_dandelion_tutorial_bcr() (in module dandelion.tutorial) setup_dandelion_tutorial_parse() (in module dandelion.tutorial) setup_dandelion_tutorial_tcr() (in module dandelion.tutorial) setup_dandelion_tutorial_trajectory() (in module dandelion.tutorial) setup_vdj_pseudobulk() (in module dandelion.base.tools) (in module dandelion.polars.tools) simplify() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

spectral_clones() (in module dandelion.external.immcantation.base.scoper) (in module dandelion.external.immcantation.polars.scoper) spectratype() (in module dandelion.base.plotting) (in module dandelion.polars.plotting) stackedbarplot() (in module dandelion.base.plotting) (in module dandelion.polars.plotting) store_germline_reference() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

T

tigger_genotype() (in module dandelion.external.immcantation.tigger) to_anndata() (dandelion.polars.core.Dandelion method) to_eager() (dandelion.polars.core.Dandelion method) to_lazy() (dandelion.polars.core.Dandelion method) to_pandas() (dandelion.polars.core.Dandelion method)

to_polars() (dandelion.polars.core.Dandelion method) to_scirpy() (in module dandelion.base.tools) (in module dandelion.polars.tools) transfer() (in module dandelion.base.tools) (in module dandelion.polars.tools)

U

update_data() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) update_metadata() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

update_plus() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

V

vdj_pseudobulk() (in module dandelion.base.tools) (in module dandelion.polars.tools) vdj_sample() (in module dandelion.base.tools) (in module dandelion.polars.tools)

vj_usage_pca() (in module dandelion.base.tools) (in module dandelion.polars.tools)

W

write() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) write_10x() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) write_airr() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method)

write_ddl() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) write_h5ddl() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) write_vdj() (dandelion.base.core.Dandelion method) (dandelion.polars.core.Dandelion method) write_zipddl() (dandelion.polars.core.Dandelion method)