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.
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
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 an introductory tutorial for new users:
We also demonstrate an enhanced analysis by integrating 10x BCR and 10x GEX data in this jupyter notebook.
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