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

## Documentation for package ‘immundata’ version 0.1.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

agg_receptors | Group AIRR sequence rows into receptors
agg_repertoires | Define biological repertoires and calculate receptor abundance
agg_strata | Group repertoires into biological strata
annotate | Add external information to ImmunData
annotate_anndata | Annotate an AnnData object from ImmunData (by barcode)
annotate_barcodes | Add external information to ImmunData
annotate_chains | Add external information to ImmunData
annotate_immundata | Add external information to ImmunData
annotate_receptors | Add external information to ImmunData
annotate_seurat | Annotate a Seurat object from ImmunData (by barcode)
assert_receptor_schema | Define which chain observations form the same receptor
collect.ImmunData | Collect ImmunData annotations
compute.ImmunData | Compute ImmunData annotations
count.ImmunData | Count chain rows in ImmunData
dimnames.ImmunData | Get Annotation Dimnames from ImmunData
dimnames<-.ImmunData | Prevent Renaming ImmunData via dimnames
downsample_immundata | Reduce repertoires to a common sampling depth
filter.ImmunData | Keep selected rows or receptors in ImmunData
filter_barcodes | Keep selected rows or receptors in ImmunData
filter_immundata | Keep selected rows or receptors in ImmunData
filter_receptors | Keep selected rows or receptors in ImmunData
from_immunarch | Convert an immunarch Object into an ImmunData Dataset
imd_drop_cols | Get input-column presets
imd_rename_cols | Get input-column presets
imd_schema | Get a standard ImmunData column name
ImmunData | ImmunData: A data structure for storing adaptive immune receptor repertoire data
make_barcode_prefix | Process chain rows while reading repertoire files
make_default_postprocessing | Process chain rows while reading repertoire files
make_default_preprocessing | Process chain rows while reading repertoire files
make_exclude_columns | Process chain rows while reading repertoire files
make_productive_filter | Process chain rows while reading repertoire files
make_receptor_schema | Define which chain observations form the same receptor
make_seq_options | Create options for comparing receptor sequences
mutate.ImmunData | Add or change annotation columns in ImmunData
mutate_immundata | Add or change annotation columns in ImmunData
names<-.ImmunData | Prevent Renaming ImmunData via names
print.ImmunData | Display the contents and biological definitions of ImmunData
read_immundata | Load an ImmunData object from disk
read_manifest | Load and Validate a Manifest for Immune Repertoire Files
read_repertoires | Read immune repertoire files into ImmunData
rename_strata | Give biological strata readable labels
test_receptor_schema | Define which chain observations form the same receptor
write_immundata | Save an ImmunData object to disk