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 and Jupyter Notebook

For a detailed use example for each Immcantation tool see the Jupyter notebook from our introductory webinar in the repository. If you don’t want to execute the Jupyter notebook yourself, you can explore a website version of it here. 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

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 Tutorial. If you don’t want to execute the Jupyter notebook yourself, you can explore a website version of it here.

We also demonstrate an enhanced analysis by integrating 10x BCR and 10x GEX data in this jupyter notebook. Explore the website version of Integration of BCR and GEX data here.

Lineage tree reconstruction

The tutorial Reconstruction and analysis of B-cell lineage trees from single cell data using Immcantation is available as a Jupyter notebook in the Immcantation bitbucket repository. A website version of the notebook is available here.

Beginning with processed single cell RNA-seq (scRNA-seq) + BCR data from 10X Genomics, 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

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

Vignettes

Detailed usage documentation and tutorials for each individual tool in Immcantation are provided in the main documentation pages for each tool. The following list of shortcuts cover common analyses. Note, each link will leave the Immcantation portal page.

• Assembling raw reads from simple Illumina sequencing protocols with pRESTO
• Assembling raw reads from 5'RACE UMI barcoded Illumina sequencing protocols with pRESTO
• Processing 10x Genomics Cell Ranger data with Change-O
• Processing IgBLAST data with Change-O
• Processing IMGT/HighV-QUEST data with Change-O
• Building lineage trees with IgPhyML
• Assigning clonal groups with SCOPer
• Basic gene usage analysis with Alakazam
• Clonality and diversity analysis with Alakazam
• Mutational load analysis with SHazaM
• Selection pressure analysis with SHazaM
• Building SHM targeting models with SHazaM
• Novel allele detection and genotyping with TIgGER