DOI: 10.18129/B9.bioc.VDJdive  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see VDJdive.

Analysis Tools for 10X V(D)J Data

Bioconductor version: 3.17

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

Author: Kelly Street [aut, cre] , Mercedeh Movassagh [aut] , Jill Lundell [aut] , Jared Brown [ctb], Linglin Huang [ctb]

Maintainer: Kelly Street <street.kelly at gmail.com>

Citation (from within R, enter citation("VDJdive")):


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biocViews Annotation, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing
Version 1.2.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2)
Imports basilisk, BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, reticulate, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils
Suggests breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
URL https://github.com/kstreet13/VDJdive
BugReports https://github.com/kstreet13/VDJdive/issues
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Source Package VDJdive_1.2.0.tar.gz
Windows Binary VDJdive_1.2.0.zip
macOS Binary (x86_64) VDJdive_1.2.0.tgz
macOS Binary (arm64) VDJdive_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/VDJdive
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VDJdive
Bioc Package Browser https://code.bioconductor.org/browse/VDJdive/
Package Short Url https://bioconductor.org/packages/VDJdive/
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