Package index • immundata

Ingestion

from_immunarch(): Convert an immunarch Object into an ImmunData Dataset

read_immundata(): Load a saved ImmunData from disk

read_metadata(): Load and Validate Metadata Table for Immune Repertoire Files

read_repertoires(): Read and process immune repertoire files to immundata

write_immundata(): Save ImmunData to disk

make_default_preprocessing() make_default_postprocessing() make_exclude_columns() make_productive_filter() make_barcode_prefix(): Preprocessing and postprocessing of input immune repertoire files

agg_receptors(): Aggregates AIRR data into receptors

agg_repertoires(): Aggregate AIRR data into repertoires

ImmunData object

ImmunData: ImmunData: A Unified Structure for Immune Receptor Repertoire Data

Transformation

annotate_immundata() annotate() annotate_receptors() annotate_barcodes() annotate_chains(): Annotate ImmunData object

filter_immundata() filter(<ImmunData>) filter_barcodes() filter_receptors(): Filter ImmunData by receptor features, barcodes or any annotations

mutate_immundata() mutate(<ImmunData>): Modify or Add Columns to ImmunData Annotations

count(<ImmunData>): Count the number of chains in ImmunData

Utils

make_receptor_schema() assert_receptor_schema() test_receptor_schema(): Create or validate a receptor schema object

make_seq_options(): Build a seq_options list for sequence‑based receptor filtering

Schema

imd_schema() imd_schema_sym() imd_meta_schema() imd_files() imd_rename_cols() imd_drop_cols() imd_repertoire_schema() imd_receptor_features() imd_receptor_chains(): Get Immundata internal schema field names