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 and SCOPer from CRAN:

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

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.

Immcantation Tutorial

For a detailed use example for each Immcantation tool see the slides and example data from our introductory webinar series. You can find a jupyter notebook version of the webinar here.

This webinar covers:

  • V(D)J gene annotation and novel polymorphism detection

  • Inference of B cell clonal relationships

  • Diversity analysis

  • Mutational load profiling

  • Modeling of somatic hypermutation (SHM) targeting

  • Quantification of selection pressure

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