VDJdive

DOI: 10.18129/B9.bioc.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 (3.17)

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")):

Installation

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

 

HTML R Script VDJdive Workflow
PDF   Reference Manual
Text   NEWS

Details

biocViews Annotation, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License Artistic-2.0
Depends R (>= 4.2)
Imports basilisk, BiocParallel, cowplot, ggplot2, gridExtra, IRanges, Matrix, methods, RColorBrewer, reticulate, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils
LinkingTo
Suggests breakaway, covr, knitr, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL https://github.com/kstreet13/VDJdive
BugReports https://github.com/kstreet13/VDJdive/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package VDJdive_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/VDJdive
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/VDJdive
Package Short Url https://bioconductor.org/packages/VDJdive/
Package Downloads Report Download Stats

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