Welcome to the Immcantation Portal!

Advances in high-throughput sequencing technologies now allow for large-scale characterization of B cell receptor (BCR) and T cell receptor (TCR) repertoires. The high germline and somatic diversity of the adaptive immune receptor repertoire (AIRR) presents challenges for biologically meaningful analysis - requiring the development of specialized computational methods.

The Immcantation framework provides a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets. Beginning from raw reads, Python and R packages are provided for pre-processing, population structure determination, and repertoire analysis.

Immcantation supports both the original Change-O standard and the new Adaptive Immune Receptor Repertoire (AIRR) standard developed by the AIRR Community (AIRR-C).

The different tools are available from PyPi, CRAN and GitHub. Versioned containers with all tools installed are hosted on Docker Hub.

Start-to-finish Workflow

Run the Immcantation packages in a single workflow to analyze your repertoire sequencing data.

Click on the image below for more details.

nf-core/airrflow Nextflow workflow using Immcantation Bulk and single-cell BCR and TCR analysis Part of the nf-core project

Core Packages

Core packages are the software tools maintained by the Immcantation team. These packages provide essential functionality for processing, analyzing, and visualizing AIRR-seq data.

Click on the images below for more details.

	Alakazam Repertoire diversity V(D)J gene usage Physicochemical property analysis Kleinstein Lab
	Amulety BCR and TCR embeddings Multiple embedding models supported Kleinstein Lab
	Change-O V(D)J alignment with IgBLAST and IMGT Kleinstein Lab
	Dowser B cell lineage trees Migration and differentiation analysis Detect ongoing evolution over time Hoehn lab
	pRESTO Bulk BCR sequence data pre-processing Read assembly and QC UMI processing Kleinstein Lab
	SCOPer Identify clonal relationships Kleinstein Lab
	SHazaM Clonal clustering threshold tuning Mutation profiling Selection pressure quantification Empirical SHM models Kleinstein Lab
	TIgGER Novel polymorphism detection Genotyping Kleinstein Lab

Contributed Packages

Contributed packages in the Immcantation ecosystem are immunoinformatics software packages developed, shared, and maintained by the community. These packages interoperate with the Immcantation framework through the AIRR Community Standard and complement Immcantation by providing specialized functionality for AIRR analysis.

Click on the images below for more details.

	IgPhyML Method to build lineage trees Mutation/selection hypothesis testing Best used via Dowser package Hoehn Lab
	RAbHIT Determination of V-D-J haplotypes Yaari Lab
	PIgLET Tools to improve genotype inference Yaari Lab
	RDI Repertoire Dissimilarity Index Kleinstein Lab
	sumrep Generate repertoire summary statistics. Visualize and comparing repertoire summaries. Matsen Group