Getting Started

Download & Installation

Installation for both the Python and R packages is performed in the usual manner.

To install pRESTO and Change-O from PyPI:

> pip3 install presto changeo --user

To install Alakazam, SHazaM, TIgGER, SCOPer and dowser from CRAN:

> R
> install.packages(c("alakazam", "shazam", "tigger", "scoper", "dowser"))

Alternatively, a complete installation of the Immcantation framework and its dependencies is available as a Docker container. Installation of the container is described in Docker Container Installation and Overview and basic usage is described in Using the Container.

Overview of B Cell Repertoire Analysis

Yaari and Kleinstein. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Medicine. 7, 121 (2015). doi:10.1186/s13073-015-0243-2