T/B cell receptor sequencing analysis notes
Please check awesome vdj too!
- A clonotype nomenclature for T cell receptors
- biostar post on integration scTCR with Seurat
- https://repseq-tutorial.readthedocs.io/en/latest/prerequisites.html
- Welcome to the Immcantation Portal Use the docker version of Immcantation if you have installation problems. 10x scBCR tutorial using Immcantation https://immcantation.readthedocs.io/en/stable/tutorials/10x_tutorial.html
- scirpy "getting started" tutorial and case study reanalysing 140k T-cells from Wu et al. (2020).
- Rep-Seq: uncovering the immunological repertoire through next-generation sequencing
- Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges
"Cool! I would start with immunarch, VDJTools, and the new scRepertoire package" -- Wʏᴀᴛᴛ MᴄDᴏɴɴᴇʟʟ from 10x genomcis
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TRUST4 developed in Shirley Liu's group. Use it to extract TCR/BCR information from bulk RNAseq or 5' scRNAseq data.
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We are happy to report a dramatic speedup for one of the core computations for adaptive immune receptor repertoire (AIRR) analysis - the discovery and counting of receptors that overlap between repertoires! Check out our CompAIRR. With 10^4 repertoires of 10^5 sequences each, CompAIRR ran in 17 minutes while the fastest existing tool took 10 days, amounting to a ~1000x speedup
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ClusTCR: a Python interface for rapid clustering of large sets of CDR3 sequences with unknown antigen specificity
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tcrdist3 is a python API-enabled toolkit for analyzing T-cell receptor repertoires
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TCRex: a web tool for the prediction of TCR–epitope recognition
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ImRex TCR-epitope recognition prediction using combined sequence input represention for convolutional neural networks.
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NetTCR - 2.0 Sequence-based prediction of peptide-TCR binding
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enclone from 10x. we should give this a try if we want to cluster TCR and BCR clonotypes.
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migec:A RepSeq processing swiss-knife.
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MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.
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tcR: an R package for T cell receptor repertoire advanced data analysis
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ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.
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Grouping of Lymphocyte Interactions by Paratope Hotspots paper: https://www.nature.com/nature/journal/v547/n7661/full/nature22976.html
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TcellMatch: Predicting T-cell to epitope specificity. cellMatch is a collection of models to predict antigen specificity of single T cells based on CDR3 sequences and other single cell modalities, such as RNA counts and surface protein counts
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scirpy: A scanpy extension for single-cell TCR analysis.
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Tessa is a Bayesian model to integrate T cell receptor (TCR) sequence profiling with transcriptomes of T cells. Enabled by the recently developed single cell sequencing techniques, which provide both TCR sequences and RNA sequences of each T cell concurrently, Tessa maps the functional landscape of the TCR repertoire, and generates insights into understanding human immune response to diseases.
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DeepTCR Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
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The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT).
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TCRdb A comprehensive database of human T-cell receptor (TCR) sequences
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Immuno-Navigator A database for gene coexpression in the immune system
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McPAS-TCR A manually curated catalogue of pathology associated T-cell receptor sequences
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@OPIGlets has built lots of lovely stuff including SAbPred, OAS, TAPhttp://opig.stats.ox.ac.uk/resources