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VDJdive
This is the released version of VDJdive; for the devel version, see VDJdive.
Analysis Tools for 10X V(D)J Data
Bioconductor version: Release (3.22)
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 iD ORCID: 0000-0001-6379-5013 , Mercedeh Movassagh [aut] ORCID iD ORCID: 0000-0001-7690-0230 , Jill Lundell [aut] ORCID iD ORCID: 0000-0002-6048-4700 , 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 "4.5") 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")
Details
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Follow Installation instructions to use this package in your R session.