VDJdive

This is the development version of VDJdive; for the stable release version, see VDJdive.

Analysis Tools for 10X V(D)J Data

Bioconductor version: Development (3.21)

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] (ORCID: ), Mercedeh Movassagh [aut] (ORCID: ), Jill Lundell [aut] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	1.9.0
In Bioconductor since	BioC 3.16 (R-4.2) (2 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
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	VDJdive_1.9.0.tar.gz
Windows Binary (x86_64)	VDJdive_1.9.0.zip (64-bit only)
macOS Binary (x86_64)	VDJdive_1.9.0.tgz
macOS Binary (arm64)	VDJdive_1.9.0.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/
Package Downloads Report	Download Stats