VDJdive
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see VDJdive.
Analysis Tools for 10X V(D)J Data
Bioconductor version: 3.19
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("VDJdive")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Annotation, ImmunoOncology, RNASeq, SingleCell, Software, TargetedResequencing |
| Version | 1.6.0 |
| 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 |
See More
| 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | VDJdive_1.6.0.zip |
| macOS Binary (x86_64) | VDJdive_1.6.0.tgz |
| macOS Binary (arm64) | VDJdive_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/VDJdive |
| Source Repository (Developer Access) | git clone [email protected]:packages/VDJdive |
| Bioc Package Browser | https://code.bioconductor.org/browse/VDJdive/ |
| Package Short Url | https://bioconductor.org/packages/VDJdive/ |
| Package Downloads Report | Download Stats |