Preprocessing: pp

assign_isotype(fasta[, org, evalue, ...])	Annotate contigs with constant region call using blastn.
assign_isotypes(fastas[, org, evalue, ...])	Annotate contigs with constant region call using blastn.
calculate_threshold(data[, mode, ...])	Calculating nearest neighbor distances for tuning clonal assignment with shazam.
create_germlines(vdj_data[, germline, org, ...])	Run CreateGermlines.py to reconstruct the germline V(D)J sequence.
check_contigs(data[, adata, ...])	Check contigs for whether they can be considered as ambiguous or not.
filter_contigs(data[, adata, filter_contig, ...])	Filter doublets and poor quality cells and corresponding contigs based on provided V(D)J DataFrame and AnnData.
format_fasta(fasta[, prefix, suffix, sep, ...])	Add prefix to the headers/contig ids in input fasta and annotation file.
format_fastas(fastas[, prefix, suffix, sep, ...])	Add prefix to the headers/contig ids in input fasta and annotation file.
quantify_mutations(data[, split_locus, ...])	Run basic mutation load analysis.
reannotate_genes(data[, igblast_db, ...])	Reannotate cellranger fasta files with igblastn and parses to airr format.
reassign_alleles(data, combined_folder[, ...])	Correct allele calls based on a personalized genotype using tigger.

Preprocessing (external): pp.external

assigngenes_igblast(fasta[, igblast_db, ...])	Reannotate with IgBLASTn.
creategermlines(airr_file[, germline, org, ...])	Wrapper for CreateGermlines.py for reconstructing germline sequences.
makedb_igblast(fasta[, igblast_output, ...])	Parse IgBLAST output to AIRR format.
parsedb_heavy(airr_file)	Parse AIRR tsv file (heavy chain contigs only).
parsedb_light(airr_file)	Parse AIRR tsv file (light chain contigs only).
recipe_scanpy_qc(adata[, layer, ...])	Recipe for running a standard scanpy QC workflow.
tigger_genotype(airr_file[, v_germline, ...])	Reassign alleles with TIgGER in R.

Tools: tl

clone_centrality(vdj_data[, verbose])	Calculate node closeness centrality in BCR/TCR network.
clone_degree(vdj_data[, weight, verbose])	Calculate node degree in BCR/TCR network.
clone_diversity(vdj_data, groupby[, method, ...])	Compute B cell clones diversity : Gini indices, Chao1 estimates, or Shannon entropy.
clone_overlap(vdj_data, groupby[, ...])	A function to tabulate clonal overlap for input as a circos-style plot.
clone_rarefaction(vdj_data, groupby[, ...])	Return rarefaction predictions for cell numbers vs clone size.
clone_size(vdj_data[, max_size, clone_key, ...])	Quantify size of clones.
define_clones(vdj_data[, dist, action, ...])	Find clones using changeo's DefineClones.py.
extract_edge_weights(vdj_data[, expanded_only])	Retrieve edge weights (BCR levenshtein distance) from graph.
find_clones(vdj_data[, identity, key, ...])	Find clones based on VDJ chain and VJ chain CDR3 junction hamming distance.
generate_network(vdj_data[, key, clone_key, ...])	Generate a Levenshtein distance network based on full length VDJ sequence alignments for heavy and light chain(s).
transfer(adata, dandelion[, expanded_only, ...])	Transfer data in Dandelion slots to AnnData object, updating the .obs, .uns, .obsm and `.obsp`slots.
setup_vdj_pseudobulk(adata[, mode, ...])	Function for prepare anndata for computing pseudobulk vdj feature space.
vdj_pseudobulk(adata[, pbs, obs_to_bulk, ...])	Function for making pseudobulk vdj feature space.
pseudotime_transfer(adata, pr_res[, suffix])	Function to add pseudotime and branch probabilities into adata.obs in place.
project_pseudotime_to_cell(adata, pb_adata, ...)	Function to project pseudotime & branch probabilities from pb_adata (pseudobulk adata) to adata (cell adata).
pseudobulk_gex(adata_raw[, pbs, ...])	Function to pseudobulk gene expression (raw count).
bin_expression(adata, bin_no, genes, ...)	Function to compute average gene expression in bins along pseudotime.
chatterjee_corr(adata, genes, pseudotime_col)	Function to compute chatterjee correlation of gene expression with pseudotime.

Plotting: pl

barplot(vdj_data, color[, palette, figsize, ...])	A barplot function to plot usage of V/J genes in the data.
clone_network(adata[, basis, edges])	Using scanpy's plotting module to plot the network.
clone_overlap(adata, groupby[, colorby, ...])	A plot function to visualise clonal overlap as a circos-style plot.
clone_rarefaction(vdj_data, color[, ...])	Plot rarefaction curve for cell numbers vs clone size.
spectratype(vdj_data, color, groupby, locus)	A spectratype function to plot usage of CDR3 length.
stackedbarplot(vdj_data, color, groupby[, ...])	A stacked bar plot function to plot usage of V/J genes in the data split by groups.

Utilities: utl

load_data(obj)	Read in or copy dataframe object and set sequence_id as index without dropping.
makeblastdb(ref)	Run makeblastdb on constant region fasta file.
read_h5ddl([filename])	Read in and returns a Dandelion class from .h5ddl format.
read_pkl([filename])	Read in and returns a Dandelion class saved using pickle format.
read_10x_airr(file[, prefix, suffix, sep, ...])	Read the 10x AIRR rearrangement .tsv directly and returns a Dandelion object.
read_10x_vdj(path[, filename_prefix, ...])	A parser to read .csv and .json files directly from folder containing 10x cellranger-outputs.
update_metadata(vdj_data[, retrieve, ...])	A Dandelion initialisation function to update and populate the .metadata slot.
concat(arrays[, check_unique, sep, ...])	Concatenate data frames and return as Dandelion object.
to_scirpy(data[, transfer, to_mudata, ...])	Convert Dandelion data to scirpy-compatible format.
from_scirpy(data)	Convert data from scirpy format to Dandelion format.
write_fasta(fasta_dict, out_fasta[, overwrite])	Generic fasta writer using fasta_iterator

Dandelion

copy()	Performs a deep copy of all slots in Dandelion class.
store_germline_reference([corrected, ...])	Update germline reference with corrected sequences and store in Dandelion object.
update_metadata([retrieve, clone_key, ...])	A Dandelion initialisation function to update and populate the .metadata slot.
update_plus([option])	Retrieve additional data columns that are useful.
write([filename, complib, compression, ...])	Writes a Dandelion class to .h5ddl format.
write_h5ddl([filename, complib, ...])	Writes a Dandelion class to .h5ddl format.
write_pkl([filename])	Writes a Dandelion class to .pkl format.
write_airr([filename])	Writes a Dandelion class to AIRR formatted .tsv format.

Logging

print_header([dependencies])	Versions that are essential for dandelion's operation.
print_versions([dependencies])	Versions that are essential for dandelion's operation.