sumrep

A summary statistic framework for BCR and TCR repertoires

Introduction

sumrep is a package for summarizing, visualizing, and comparing immune receptor repertoires. It contains dozens of different summary statistics to be applied on various levels of assumptions, from raw query reads to inferred phylogenies, as well as easy and principled ways to plot and compare repertoires. It currently supports the IgH, IgL, IgK, TRA, and TRB loci.

Instructions for getting and using sumrep can be found via the following pages:

• Installation - Steps for installing sumrep and optional annotation and simulation tools
• Docker image - Instructions for using Docker to obtain a readily usable version of sumrep in a controlled environment
• Usage - Quickstart on how to use sumrep to analyze and gain insights from your data, including examples
• Extended documentation - In-depth breakdown of data specifications and functionality
• FAQ - Frequently asked questions about sumrep

A paper describing sumrep can be found here. Please cite this publication if you use sumrep for your analysis.

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