Overview
Installation
Required database
External softwares
Basic requirements
Acknowledgements
Tutorial:
Pre-processing
Filtering
Cellranger V4 onwards
BCR clustering
Interoperability with
scirpy
dandelion
scirpy
Visualizing BCR data
Calculating diversity and mutation
Dandelion
class
Running from R
API:
Preprocessing:
pp
Preprocessing (external):
pp.external
Tools:
tl
Plotting:
pl
Utilities:
utl
Dandelion
Logging
dandelion
»
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
L
|
M
|
P
|
Q
|
R
|
S
|
T
|
U
|
W
_
__init__() (dandelion.utilities.Dandelion method)
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)
C
calculate_threshold() (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 (class in dandelion.utilities)
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_bcr() (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)
Q
quantify_mutations() (in module dandelion.preprocessing)
R
read_10x_airr() (in module dandelion.utilities)
read_h5() (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
spectratype() (in module dandelion.plotting)
stackedbarplot() (in module dandelion.plotting)
T
tigger_genotype() (in module dandelion.preprocessing.external)
to_scirpy() (in module dandelion.utilities)
transfer() (in module dandelion.tools)
U
update_germline() (dandelion.Dandelion method)
update_metadata() (in module dandelion.utilities)
W
write_h5() (dandelion.Dandelion method)
write_pkl() (dandelion.Dandelion method)