API reference#
Note
The API is filling in phase by phase. Module pages are added here as each subpackage
lands (vdjtools.model, vdjtools.stats, vdjtools.features, …).
vdjtools#
vdjtools — TCR/BCR immune-repertoire analysis (v2; Python + C++).
A clean-room rewrite of the legacy Groovy/Java vdjtools, standardised on the AIRR
schema and polars DataFrames with minimal object-orientation, built on the
antigenomics ecosystem (seqtree, vdjmatch, arda).
Native hot loops — the V(D)J Pgen dynamic program, the generation sampler, and the
EM E-step — live in the compiled vdjtools._core extension. Everything else is
pure polars/numpy. Subpackages (io, model, stats, features, overlap,
preprocess, biomarker, sc) are imported explicitly by the caller so that
import vdjtools never pays the cost of heavy optional dependencies (arda/mmseqs2,
vdjmatch/seqtree) until a feature that needs them is used.