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

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Documentation for package ‘immundata’ version 0.0.7

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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