Immcantation Tutorials

Each tool in the framework has its own documentation site, with detailed usage information and examples. A good starting point to familiarize yourself with the framework is to follow one the tutorials listed here. They are available as Jupyter notebooks under the folder training in the Immcantation Bitbucket repository.

Introductory Webinar

Start here: Introductory Webinar and Jupyter Notebook

For a detailed use example for each Immcantation follow the tutorial Introduction to B cell repertoire analysis using the Immcantation framework. This tutorial is based on our introductory webinar. It is also available as a Jupyter notebook (intro-lab.ipynb) in the Immcantation repository.

Tutorial

Introduction to B cell repertoire analysis using the Immcantation framework 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

Single-cell Analysis

10x Genomics V(D)J Sequence Analysis with Immcantation Tutorial

For information on how to process 10x Genomics VDJ data to be analyzed with Immcantation, we offer the introductory tutorial 10x Genomics V(D)J Sequence Analysis with Immcantation. It is available as a Jupyter notebook (10x_tutorial.ipynb) in the Immcantation repository.

Tutorial

10x Genomics V(D)J Sequence Analysis with Immcantation covers:

  • V(D)J gene annotation

  • Inference of clonal relationships

  • Lineage tree reconstruction

  • Incorporation of Cell Ranger annotations

Integration of BCR and GEX data

In Integration of BCR and GEX data we demonstrate an enhanced analysis by integrating 10x BCR and 10x GEX data. The jupyter notebook (BCR_Seurat_tutorial.ipynb) is available in the Immcantation repository.

Tutorial

Integration of BCR and GEX data covers:

  • Integration of BCR data with the GEX Seurat object

  • Highlight BCR cells in the GEX UMAP

  • Integration of GEX cell annotations in the BCR data

  • Identify GEX clusters in the BCR UMAP

  • Highlight other BCR features in UMAPs

Lineage tree reconstruction

Reconstruction and analysis of B-cell lineage trees from single cell data using Immcantation

The tutorial Reconstruction and analysis of B-cell lineage trees from single cell data using Immcantation is available as a Jupyter notebook (dowser_tutorial.ipynb) in the Immcantation repository.

Tutorial

Beginning with processed single cell RNA-seq (scRNA-seq) + BCR data from 10X Genomics, with Reconstruction and analysis of B-cell lineage trees from single cell you will learn:

  • how cell type annotations can be associated with BCR sequences,

  • how clonal clusters can be identified, and

  • how B cell phylogenetic trees can be built and visualized using these data sources.

Video presentations

Link to Immcantation's YouTube Channel

You can watch presentations by Immcantation developers and users in Immcantation’s YouTube channel.