kstreet13/VDJdive: Analysis Tools for 10X V(D)J Data

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.

Getting started

Package details

Bioconductor views Annotation ImmunoOncology RNASeq SingleCell Software TargetedResequencing
URL https://github.com/kstreet13/VDJdive
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
kstreet13/VDJdive documentation built on May 31, 2024, 1:26 p.m.