📚 Tools and databases for analyzing HLA and VDJ genes.
Accurate Typing of Diverse Immune-Related Gene Families from Long-Read Sequencing Data. It can handle HLA, KIR, IG, TCR, CYP gene families. It supports both WGS and amplicon data. It supports PacBio and Nanopore data.
An R package to analyze single-cell V(D)J data
Fast simulator of BCR and TCR sequences with full ground-truth annotations: V(D)J recombination, somatic hypermutation and sequencing artifacts across 23 species. Rust core with a Python API, for training and benchmarking AIRR-seq tools.
Alignment-free graph models of TCR and BCR repertoires built from Lempel-Ziv and FlashBack string decompositions. Compute sequence generation probability (Pgen) and repertoire diversity, and generate new sequences. Python with a C core.
🧽 Estimate sequencing saturation for GEX, VDJ, and ADT data from the 10x Genomics platform.
Construction of IHGV sequences from RNA-seq
A three-part R tutorial for single-cell BCR sequence processing and integration with gene expression data, using Immcantation and Seurat
Deep-learning V(D)J aligner for BCR and TCR sequences. A single model predicts V/D/J allele calls, segment boundaries and the junction, with AIRR-format output. Published in Nucleic Acids Research (2025).
Extract TCR and BCR clonotypes from raw sequencing data. Alignment against germline gene databases, error correction, receptor assembly, and clonotype grouping — turning FASTQ into a quantified repertoire with full QC.
VirtualDJ — это популярное программное обеспечение для сведение музыки, создания миксов и проведения живых диджейских сетов. Приложение предлагает интуитивный интерфейс с двумя или четырьмя деками, встроенные эффекты, автосинхронизацию темпа и подгонку тональности, что делает его отличным выбором как для новичков, так и для профи.
Tool to analyze and visualize scRNA-Seq data with focus on 10x VDJ assay.
Run various bioinformatics software for classifying the immune repertoire from bulk RNAseq
Imports V(D)J data from various formats, including MiXCR, immunoSeq, AiRR and more (bulk or single-cell) and normalizes them into one standard clonotype dataset that every downstream
Matches clonotypes between two V(D)J datasets — typically a deep bulk dataset and a smaller single-cell reference — so any property from the reference becomes available on the matched bulk clonotypes.
Calculates V and J gene segment usage frequencies across samples, plus their pairwise combinations, revealing the germline biases that antigen exposure, vaccination, and disease leave behind.
V(D)J T Cell and B Cell Analysis with cellranger vdj
Re-groups an existing V(D)J dataset by a definition you choose — any combination of V gene, J gene, and CDR3 sequence — picks a representative for each new group, and recalculates every abundance column by summing across the members.
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