Package: immundata 0.0.5

Vadim I. Nazarov

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

Provides a unified data layer for single-cell, spatial and bulk T-cell and B-cell immune receptor repertoire data. Think AnnData or SeuratObject, but for AIRR data, a.k.a. Adaptive Immune Receptor Repertoire, VDJ-seq, RepSeq, or VDJ sequencing data.

Authors:Vadim I. Nazarov [aut, cre]

immundata_0.0.5.tar.gz
immundata_0.0.5.zip(r-4.7)immundata_0.0.5.zip(r-4.6)immundata_0.0.5.zip(r-4.5)
immundata_0.0.5.tgz(r-4.6-any)immundata_0.0.5.tgz(r-4.5-any)
immundata_0.0.5.tar.gz(r-4.7-any)immundata_0.0.5.tar.gz(r-4.6-any)
immundata_0.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
immundata/json (API)

# Install 'immundata' in R:
install.packages('immundata', repos = c('https://immunomind.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immunomind/immundata/issues

On CRAN:

Conda:

airrbioinformaticsdata-engineeringimmune-repertoireimmunomicsimmunotherapyvaccine

4.30 score 2 stars 1 packages 3 scripts 1.6k downloads 38 exports 51 dependencies

Last updated from:c8ee9183e8. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING218
source / vignettesOK245
linux-release-x86_64WARNING231
macos-release-arm64WARNING226
macos-oldrel-arm64WARNING205
windows-develWARNING157
windows-releaseWARNING167
windows-oldrelWARNING147
wasm-releaseOK180

Exports:agg_receptorsagg_repertoiresannotateannotate_barcodesannotate_chainsannotate_immundataannotate_receptorsannotate_seuratassert_receptor_schemafilter_barcodesfilter_immundatafilter_receptorsfrom_immunarchget_test_idataget_test_immundataimd_drop_colsimd_filesimd_meta_schemaimd_receptor_chainsimd_receptor_featuresimd_rename_colsimd_repertoire_schemaimd_schemaimd_schema_symImmunDatamake_barcode_prefixmake_default_postprocessingmake_default_preprocessingmake_exclude_columnsmake_productive_filtermake_receptor_schemamake_seq_optionsmutate_immundataread_immundataread_metadataread_repertoirestest_receptor_schemawrite_immundata

Dependencies:backportsbitbit64blobcachemcheckmateclicliprcollectionscpp11crayonDBIdbplyrdplyrduckdbduckplyrfarverfastmapgenericsggplot2gluegtablehmsisobandjsonlitelabelinglifecyclemagrittrmemoisepillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Aggregates AIRR data into receptorsagg_receptors
Aggregate AIRR data into repertoiresagg_repertoires
Annotate ImmunData objectannotate annotate_barcodes annotate_chains annotate_immundata annotate_receptors
Annotate a Seurat object from ImmunData (by barcode)annotate_seurat
Count the number of chains in ImmunDatacount.ImmunData
Filter ImmunData by receptor features, barcodes or any annotationsfilter.ImmunData filter_barcodes filter_immundata filter_receptors
Convert an immunarch Object into an ImmunData Datasetfrom_immunarch
Get Immundata internal schema field namesimd_drop_cols imd_files imd_meta_schema imd_receptor_chains imd_receptor_features imd_rename_cols imd_repertoire_schema imd_schema imd_schema_sym
ImmunData: A Unified Structure for Immune Receptor Repertoire DataImmunData
Preprocessing and postprocessing of input immune repertoire filesmake_barcode_prefix make_default_postprocessing make_default_preprocessing make_exclude_columns make_productive_filter
Create or validate a receptor schema objectassert_receptor_schema make_receptor_schema test_receptor_schema
Build a 'seq_options' list for sequence‑based receptor filteringmake_seq_options
Modify or Add Columns to ImmunData Annotationsmutate.ImmunData mutate_immundata
Load a saved ImmunData from diskread_immundata
Load and Validate Metadata Table for Immune Repertoire Filesread_metadata
Read and process immune repertoire files to immundataread_repertoires
Save ImmunData to diskwrite_immundata