# A Unified Data Layer for Large-Scale Single-Cell, Spatial and Bulk Immunomics

## Documentation for package ‘immundata’ version 0.0.7

- DESCRIPTION file.

## Help Pages

agg_receptors | Aggregates AIRR data into receptors
agg_repertoires | Aggregate AIRR data into repertoires
agg_strata | Aggregate repertoires into strata
annotate | Annotate ImmunData object
annotate_anndata | Annotate an AnnData object from ImmunData (by barcode)
annotate_barcodes | Annotate ImmunData object
annotate_chains | Annotate ImmunData object
annotate_immundata | Annotate ImmunData object
annotate_receptors | Annotate ImmunData object
annotate_seurat | Annotate a Seurat object from ImmunData (by barcode)
assert_receptor_schema | Create or validate a receptor schema object
collect.ImmunData | Collect ImmunData annotations
compute.ImmunData | Compute ImmunData annotations
count.ImmunData | Count the number of chains in ImmunData
dimnames.ImmunData | Get Annotation Dimnames from ImmunData
dimnames<-.ImmunData | Prevent Renaming ImmunData via dimnames
downsample_immundata | Downsample ImmunData annotations at the repertoire level
filter.ImmunData | Filter ImmunData by receptor features, barcodes or any annotations
filter_barcodes | Filter ImmunData by receptor features, barcodes or any annotations
filter_immundata | Filter ImmunData by receptor features, barcodes or any annotations
filter_receptors | Filter ImmunData by receptor features, barcodes or any annotations
from_immunarch | Convert an immunarch Object into an ImmunData Dataset
imd_drop_cols | Get Immundata internal schema field names
imd_files | Get Immundata internal schema field names
imd_meta_schema | Get Immundata internal schema field names
imd_receptor_chains | Get Immundata internal schema field names
imd_receptor_features | Get Immundata internal schema field names
imd_rename_cols | Get Immundata internal schema field names
imd_repertoire_schema | Get Immundata internal schema field names
imd_schema | Get Immundata internal schema field names
imd_schema_sym | Get Immundata internal schema field names
ImmunData | ImmunData: A Unified Structure for Immune Receptor Repertoire Data
make_barcode_prefix | Preprocessing and postprocessing of input immune repertoire files
make_default_postprocessing | Preprocessing and postprocessing of input immune repertoire files
make_default_preprocessing | Preprocessing and postprocessing of input immune repertoire files
make_exclude_columns | Preprocessing and postprocessing of input immune repertoire files
make_productive_filter | Preprocessing and postprocessing of input immune repertoire files
make_receptor_schema | Create or validate a receptor schema object
make_seq_options | Build a 'seq_options' list for sequence‑based receptor filtering
mutate.ImmunData | Modify or Add Columns to ImmunData Annotations
mutate_immundata | Modify or Add Columns to ImmunData Annotations
names<-.ImmunData | Prevent Renaming ImmunData via names
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
rename_strata | Rename strata labels
test_receptor_schema | Create or validate a receptor schema object
write_immundata | Save ImmunData to disk