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.
The Immcantation Lab container¶
Information on obtaining and using the container with the Jupyter notebooks and data needed to follow the Immcantation tutorials can be found within the general guide.
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 a Jupyter notebook (intro-lab.ipynb) in the Immcantation repository.
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
Mutational load profiling
Modeling of somatic hypermutation (SHM) targeting
Quantification of selection pressure
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.
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
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.
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¶
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.
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.
You can watch presentations by Immcantation developers and users in Immcantation’s YouTube channel.
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