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Overview
Installation
Basic requirements
Acknowledgements
Support
Citation
References
Tutorial:
Singularity preprocessing
Loading data for analysis
V(D)J analysis
Singularity changeo clonotype calling
V(D)J pseudobulk feature space
Advanced Guide:
Pre-processing (Re-annotation)
Reading 10X Cell Ranger output directly
Interoperability with
scirpy
Filtering
V(D)J clustering
Visualizing V(D)J data
Calculating diversity and mutation
Analyzing TCR data
V(D)J Trajectory
Dandelion class
Running from R
API:
Preprocessing:
pp
Preprocessing (external):
pp.external
Tools:
tl
Plotting:
pl
Utilities:
utl
Dandelion
Logging
dandelion
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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L
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M
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P
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Q
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R
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S
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T
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U
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V
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W
A
assign_isotype() (in module dandelion.preprocessing)
assign_isotypes() (in module dandelion.preprocessing)
assigngenes_igblast() (in module dandelion.preprocessing.external)
B
barplot() (in module dandelion.plotting)
bin_expression() (in module dandelion.tools)
C
calculate_threshold() (in module dandelion.preprocessing)
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.preprocessing.external)
D
dandelion.Dandelion
module
dandelion.logging
module
dandelion.plotting
module
dandelion.preprocessing
module
dandelion.preprocessing.external
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)
L
load_data() (in module dandelion.utilities)
M
makeblastdb() (in module dandelion.utilities)
makedb_igblast() (in module dandelion.preprocessing.external)
module
dandelion.Dandelion
dandelion.logging
dandelion.plotting
dandelion.preprocessing
dandelion.preprocessing.external
dandelion.tools
dandelion.utilities
P
parsedb_heavy() (in module dandelion.preprocessing.external)
parsedb_light() (in module dandelion.preprocessing.external)
print_header() (in module dandelion.logging)
print_versions() (in module dandelion.logging)
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.preprocessing)
R
read_10x_airr() (in module dandelion.utilities)
read_10x_vdj() (in module dandelion.utilities)
read_h5ddl() (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.preprocessing.external)
S
setup_vdj_pseudobulk() (in module dandelion.tools)
spectratype() (in module dandelion.plotting)
stackedbarplot() (in module dandelion.plotting)
store_germline_reference() (dandelion.Dandelion method)
T
tigger_genotype() (in module dandelion.preprocessing.external)
to_scirpy() (in module dandelion.utilities)
transfer() (in module dandelion.tools)
U
update_metadata() (dandelion.Dandelion method)
(in module dandelion.utilities)
update_plus() (dandelion.Dandelion method)
V
vdj_pseudobulk() (in module dandelion.tools)
W
write() (dandelion.Dandelion method)
write_airr() (dandelion.Dandelion method)
write_fasta() (in module dandelion.utilities)
write_h5ddl() (dandelion.Dandelion method)
write_pkl() (dandelion.Dandelion method)
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