A Unified Data Layer for Large-Scale Single-Cell, Spatial and
Bulk Immunomics
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Documentation for package ‘immundata’ version 0.1.0
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 |