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  • BRAPeS (BCR Reconstruction Algorithm for Paired-End Single-cell), software for reconstruction of B cell receptors (BCR) using short, paired-end single-cell RNA-sequencing.

    • Publications
    • "Reconstructing B-cell receptor sequences from short-read single-cell RNA sequencing with BRAPeS"
      DOI: 10.26508/lsa.201900371, Published: 2019-08-26, Citations: 10
    • Preprints
    • "Reconstructing B cell receptor sequences from short-read single cell RNA-sequencir with BRAPeS"
      DOI: 10.1101/389999, Citations: 0
  • Platform: Python
  • Code: https://github.com/YosefLab/BRAPeS
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  • License: Custom
  • Categories: Alignment, Immune
  • Added: 2018-08-24, Updated: 2018-08-24

C

  • Change-O is a collection of tools for processing the output of V(D)J alignment tools (e.g. IMGT/HighV-QUEST and IgBLAST), assigning clonal clusters to immunoglobulin sequences, and reconstructing germline sequences. This tool is part of the Immcantation software suite.

    • Publications
    • "Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data"
      DOI: 10.1093/bioinformatics/btv359, Published: 2015-06-10, Citations: 791
  • Platform: Python
  • Code: https://github.com/immcantation/changeo
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  • License: AGPL-3.0
  • Categories: Alignment, Immune
  • Added: 2025-04-12, Updated: 2025-04-12

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  • MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling. It supports all kinds of single cell platforms and technologies for immune profiling, including commercial vendors such as 10x Genomics or BD Rhapsody and any custom protocol (droplet-based, plate-based, combinatorial barcoding etc.). Check more at https://docs.milaboratories.com.

    • Publications
    • "Antigen receptor repertoire profiling from RNA-seq data"
      DOI: 10.1038/nbt.3979, Published: 2017-10-11, Citations: 276
    • "MiXCR: software for comprehensive adaptive immunity profiling"
      DOI: 10.1038/nmeth.3364, Published: 2015-04-29, Citations: 1504
  • Platform: Java/Kotlin
  • Code: https://github.com/milaboratory/mixcr
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  • License: Custom
  • Categories: Alignment, Allele Specific, Assembly, Clustering, Immune, UMIs
  • Added: 2022-12-25, Updated: 2022-12-25

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  • The REpertoire Sequencing TOolkit (pRESTO) is composed of a suite of utilities to handle all stages of raw sequence processing prior to alignment against reference germline sequences (germline segment assignment). This tool is part of the Immcantation software suite.

    • Publications
    • "pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires"
      DOI: 10.1093/bioinformatics/btu138, Published: 2014-03-10, Citations: 449
  • Platform: Python
  • Code: https://github.com/immcantation/presto
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  • License: AGPL-3.0
  • Categories: Alignment, Immune, UMIs
  • Added: 2025-04-12, Updated: 2025-04-12

S

  • SCOPer (Spectral Clustering for clOne Partitioning) provides a computational framework for the identification of B cell clonal relationships from Adaptive Immune Receptor Repertoire sequencing data. This tool is part of the Immcantation software suite.

    • Publications
    • "A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data"
      DOI: 10.1093/bioinformatics/bty235, Published: 2018-06-27, Citations: 79
    • Preprints
    • "Performance-optimized partitioning of clonotypes from high-throughput immunoglobulin repertoire sequencing data"
      DOI: 10.1101/175315, Citations: 1
  • Platform: R/C++
  • Code: https://github.com/immcantation/scoper
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  • License: AGPL-3.0
  • Categories: Clustering, Immune, Visualisation
  • Added: 2025-04-12, Updated: 2025-04-12

  • Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure

    • Publications
    • "STREAK: A supervised cell surface receptor abundance estimation strategy for single cell RNA-sequencing data using feature selection and thresholded gene set scoring"
      DOI: 10.1371/journal.pcbi.1011413, Published: 2023-08-21, Citations: 3
    • Preprints
    • "STREAK: A Supervised Cell Surface Receptor Abundance Estimation Strategy for Single Cell RNA-Sequencing Data using Feature Selection and Thresholded Gene Set Scoring"
      DOI: 10.1101/2022.11.10.516050, Citations: 0
  • Platform: R
  • Code: https://CRAN.R-project.org/package=STREAK
  • License: GPL-2.0-or-later
  • Categories: Immune
  • Added: 2022-12-09, Updated: 2024-01-05

  • This project is an implementation of a pipeline for Single-cell RNAseq package for recovering TCR data in python.
  • Platform: Python
  • Code: https://github.com/ElementoLab/scTCRseq
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  • License: AGPL-3.0
  • Categories: Immune
  • Added: 2017-09-09, Updated: 2021-06-28

T

  • TRAPeS (TCR Reconstruction Algorithm for Paired-End Single-cell), software for reconstruction of T cell receptors (TCR) using short, paired-end single-cell RNA-sequencing.

    • Publications
    • "Targeted reconstruction of T cell receptor sequence from single cell RNA-seq links CDR3 length to T cell differentiation state"
      DOI: 10.1093/nar/gkx615, Published: 2017-07-17, Citations: 74
    • Preprints
    • "Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state"
      DOI: 10.1101/072744, Citations: 5
  • Platform: Python
  • Code: https://github.com/yoseflab/trapes
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  • License: Custom
  • Categories: Immune, Quantification
  • Added: 2016-11-10, Updated: 2017-09-09

V

  • This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline
  • Platform: R
  • Code: https://github.com/kstreet13/VDJdive
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  • License: Artistic-2.0
  • Categories: Immune, Integration, Visualisation
  • Added: 2022-11-04, Updated: 2022-11-04

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