VDJdive

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see VDJdive.

Analysis Tools for 10X V(D)J Data

Bioconductor version: 3.18

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], Mingzhi Ye [ctb]

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

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("VDJdive")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("VDJdive")

VDJdive Workflow HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing

Version 1.4.0

In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)

License Artistic-2.0

Depends R (>= 4.2)

Imports BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, Rcpp, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils

System Requirements

URL https://github.com/kstreet13/VDJdive

Bug Reports https://github.com/kstreet13/VDJdive/issues

Suggests breakaway, covr, knitr, rmarkdown, testthat, BiocStyle

Linking To Rcpp

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

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