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 Notebooks under the folder training in the Immcantation Bitbucket repository.

The Immcantation Lab container

How to use the Immcantation Lab container

Information on obtaining and using the container with the notebooks and data needed to follow the Immcantation tutorials can be found within the general guide.

Introduction to B cell repertoire analysis

Start here: Introductory tutorial and R Notebook

For a detailed use example for each Immcantation tool 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 an R Notebook (intro-lab.Rmd) 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

  • Lineage tree reconstruction

  • 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 an R Notebook (10x_tutorial.Rmd) in the Immcantation repository.

Tutorial

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

  • V(D)J gene annotation

  • Inference of clonal relationships

  • V gene Somatic Hypermutation (SHM) frequency

  • 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 R Notebook (BCR_Seurat_tutorial.Rmd) 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

Video presentations

Link to Immcantation's YouTube Channel

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.