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.

presto-img

https://img.shields.io/pypi/dm/presto

pRESTO

  • Quality control

  • Read assembly

  • UMI processing

  • Error profiling

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https://img.shields.io/pypi/dm/changeo

Change-O

  • V(D)J reference alignment standardization

  • Clonal clustering

  • Germline reconstruction

  • Conversion and annotation

alakazam-img

https://cranlogs.r-pkg.org/badges/alakazam

Alakazam

  • Clonal lineage reconstruction

  • Lineage topology analysis

  • Repertoire diversity

  • V(D)J gene usage

  • Physicochemical property analysis

shazam-img

https://cranlogs.r-pkg.org/badges/shazam

SHazaM

  • Mutation profiling

  • Selection pressure quantification

  • Empirical SHM models

  • Chimera detection

  • Clonal clustering threshold tuning

tigger-img

https://cranlogs.r-pkg.org/badges/tigger

TIgGER

  • Novel polymorphism detection

  • Genotyping

scoper-img

https://cranlogs.r-pkg.org/badges/scoper

SCOPer

  • Spectral clonal clustering methods

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prestoR

  • pRESTO report generation

dowser-img

https://cranlogs.r-pkg.org/badges/dowser

dowser

  • Phylogenetic analysis on B cell receptor repertoires

Contributed Packages

Click on the images below for more details.

rdi-img

RDI

  • Repertoire Dissimilarity Index

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RAbHIT

  • Determination of V-D-J haplotypes

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IgPhyML

  • Clonal lineage tree construction

  • Mutation/selection hypothesis testing

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sumrep

  • Generate repertoire summary statistics.

  • Visualize and comparing repertoire summaries.