Important

Are you an Immcantation user and/or interested in adaptive immune receptor repertoire analysis?

Register now for the upcoming Immcantation Users Group Meeting! It will be held virtually on January 30th, 2025, from 10 to 1:30pm (ET). All talks will be from user-submitted abstracts.

Full information here: https://immcantation.github.io/users-meeting/

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 provide 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.

https://img.shields.io/static/v1?label=AIRR-C%20sw-tools%20v1&message=compliant&color=008AFF&labelColor=000000&style=plastic

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

https://img.shields.io/docker/pulls/immcantation/suite

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

Core Packages

Click on the images below for more details.

alakazam

downloads

Alakazam

  • Repertoire diversity

  • V(D)J gene usage

  • Physicochemical property analysis

Change-O

downloads

Change-O

  • V(D)J alignment with IgBLAST and IMGT

dowser

downloads

Dowser

  • B cell lineage trees

  • Migration and differentiation analysis

  • Detect ongoing evolution over time

pRESTO

downloads

pRESTO

  • Bulk BCR sequence data pre-processing

  • Read assembly and QC

  • UMI processing

SCOPer

downloads

SCOPer

  • Identify clonal relationships

SHazaM

downloads

SHazaM

  • Clonal clustering threshold tuning

  • Mutation profiling

  • Selection pressure quantification

  • Empirical SHM models

TIgGER

downloads

TIgGER

  • Novel polymorphism detection

  • Genotyping

Contributed Packages

Click on the images below for more details.

IgPhyML

IgPhyML

  • Method to build lineage trees

  • Mutation/selection hypothesis testing

  • Best used via Dowser package

RAbHIT

RAbHIT

  • Determination of V-D-J haplotypes

PIgLET

PIgLET

  • Tools to improve genotype inference

RDI

RDI

  • Repertoire Dissimilarity Index

sumrep

sumrep

  • Generate repertoire summary statistics.

  • Visualize and comparing repertoire summaries.