This is the development version of VDJdive; for the stable release version, see VDJdive.
Analysis Tools for 10X V(D)J DataBioconductor version: Development (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: 0000-0001-6379-5013 , Mercedeh Movassagh [aut] ORCID: 0000-0001-7690-0230 , Jill Lundell [aut] ORCID: 0000-0002-6048-4700 , Jared Brown [ctb], Linglin Huang [ctb], Mingzhi Ye [ctb]
Maintainer: Kelly Street <street.kelly at gmail.com>
Citation (from within R, entercitation("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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("VDJdive")Follow Installation instructions to use this package in your R session.
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