Package: immundata 0.1.0

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_0.1.0.tar.gz
immundata_0.1.0.zip(r-4.7-any)immundata_0.1.0.zip(r-4.6-any)immundata_0.1.0.zip(r-4.5-any)
immundata_0.1.0.tgz(r-4.6-any)immundata_0.1.0.tgz(r-4.5-any)
immundata_0.1.0.tar.gz(r-4.7-any)immundata_0.1.0.tar.gz(r-4.6-any)
immundata_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
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:

airrbioinformaticsbiomarker-discoverydata-engineeringimmune-repertoireimmunomicsimmunotherapyvaccine

4.51 score 3 stars 1 packages 30 scripts 1.2k downloads 41 exports 42 dependencies

Last updated from:0a70309881. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK281
source / vignettesOK262
linux-releaseOK272
macos-releaseOK234
macos-oldrelOK319
windows-develOK230
windows-releaseOK226
windows-oldrelOK250
wasm-releaseOK163

Exports:agg_receptorsagg_repertoiresagg_strataannotateannotate_anndataannotate_barcodesannotate_chainsannotate_immundataannotate_receptorsannotate_seuratassert_receptor_schemadownsample_immundatafilter_barcodesfilter_immundatafilter_receptorsfrom_immunarchget_test_idataimd_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_manifestread_repertoiresrename_stratatest_receptor_schemawrite_immundata

Dependencies:backportsbitbit64blobcachemcheckmateclicliprcollectionscpp11crayonDBIdbplyrdplyrduckdbduckplyrfastmapgenericsgluehmsjsonlitelifecyclemagrittrmemoisepillarpkgconfigprettyunitsprogresspurrrR6readrrlangstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithr

Readme and manuals

Help Manual

Help pageTopics
Group AIRR sequence rows into receptorsagg_receptors
Define biological repertoires and calculate receptor abundanceagg_repertoires
Group repertoires into biological strataagg_strata
Annotate an AnnData object from ImmunData (by barcode)annotate_anndata
Add external information to ImmunDataannotate annotate_barcodes annotate_chains annotate_immundata annotate_receptors
Annotate a Seurat object from ImmunData (by barcode)annotate_seurat
Collect ImmunData annotationscollect.ImmunData
Compute ImmunData annotationscompute.ImmunData
Count chain rows in ImmunDatacount.ImmunData
Get Annotation Dimnames from ImmunDatadimnames.ImmunData
Prevent Renaming ImmunData via dimnamesdimnames<-.ImmunData
Reduce repertoires to a common sampling depthdownsample_immundata
Keep selected rows or receptors in ImmunDatafilter.ImmunData filter_barcodes filter_immundata filter_receptors
Convert an immunarch Object into an ImmunData Datasetfrom_immunarch
Get input-column presetsimd_drop_cols imd_rename_cols
Get a standard ImmunData column nameimd_schema
ImmunData: A data structure for storing adaptive immune receptor repertoire dataImmunData
Process chain rows while reading repertoire filesmake_barcode_prefix make_default_postprocessing make_default_preprocessing make_exclude_columns make_productive_filter
Define which chain observations form the same receptorassert_receptor_schema make_receptor_schema test_receptor_schema
Create options for comparing receptor sequencesmake_seq_options
Add or change annotation columns in ImmunDatamutate.ImmunData mutate_immundata
Prevent Renaming ImmunData via namesnames<-.ImmunData
Display the contents and biological definitions of ImmunDataprint.ImmunData
Load an ImmunData object from diskread_immundata
Load and Validate a Manifest for Immune Repertoire Filesread_manifest
Read immune repertoire files into ImmunDataread_repertoires
Give biological strata readable labelsrename_strata
Save an ImmunData object to diskwrite_immundata