T/BCR-seq-analysis
T/B cell receptor sequencing analysis notes
Please check awesome vdj too!
tutorials
- A clonotype nomenclature for T cell receptors
- T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
- 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).
- Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease
papers
- Can we predict T cell specificity with digital biology and machine learning?
- reivew High-throughput and single-cell T cell receptor sequencing technologies
- Disease diagnostics using machine learning of immune receptors
- Rep-Seq: uncovering the immunological repertoire through next-generation sequencing
- Single Cell T Cell Receptor Sequencing: Techniques and Future Challenges
- T-cell repertoire analysis and metrics of diversity and clonality
- TCR-Vγδ usage distinguishes protumor from antitumor intestinal γδ T cell subsets
- De novo prediction of cancer-associated T cell receptors for noninvasive cancer detection
- TCR-engineered T cell therapy in solid tumors: State of the art and perspectives
simulation
Echidna: Integrated simulations of single-cell immune receptor repertoires and transcriptomes
Tools
"Cool! I would start with immunarch, VDJTools, and the new scRepertoire package" -- Wʏᴀᴛᴛ MᴄDᴏɴɴᴇʟʟ from 10x genomcis
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dandelion python package for analyzing single cell BCR/TCR data from 10x Genomics 5’ solution!
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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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Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq 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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GraphMHC: neoantigen prediction model applying the graph neural network to molecular structure" A hybrid graph attention network + CNN to predict peptides that bind MHC proteins
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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 https://twitter.com/John_Will_I_Am/status/1570837756787691527 https://www.science.org/doi/10.1126/sciadv.abq5089
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Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
machine learning
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STAPLER: Efficient learning of TCR-peptide specificity prediction from full-length TCR-peptide data
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Structure-based prediction of T cell receptor:peptide-MHC interactions Preprint from Philip Bradley where he creates a version of AlphaFold to model TCR:peptide-MHC interactions. Benchmark is far from perfect, but the paper shows that deep learning-based structural modelling is a possible strategy to predict TCR specificity.
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Uni-Fold: an open-source platform for developing protein models beyond AlphaFold. https://github.com/dptech-corp/Uni-Fold
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Equidock: docking protein receptor and ligand https://github.com/octavian-ganea/equidock_public news https://news.mit.edu/2022/ai-predicts-protein-docking-0201
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AlphaFill: enriching AlphaFold models with ligands and cofactors
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DeepMind AlphaFold for antibody discovery: What's the status?
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Why AlphaFold won’t revolutionise drug discovery We made AlphaFold dream of new protein assemblies, used #ProteinMPNN to bring it back to reality. https://twitter.com/BasileWicky/status/1570564831522213888
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Here, we introduce OmegaFold, the first computational method to successfully predict high-resolution protein structure from a single primary sequence alone. Using a new combination of a protein language model that allows us to make predictions from single sequences and a geometry-inspired transformer model trained on protein structures, OmegaFold outperforms RoseTTAFold and achieves similar prediction accuracy to AlphaFold2 on recently released structures.
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Learning inverse folding from millions of predicted structures https://twitter.com/alexrives/status/1513603415959556096
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[PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction}(https://arxiv.org/abs/2206.12240)
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Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling https://twitter.com/DingXiaozhe/status/1618257727515676672
database
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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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hlabud provides methods to retrieve sequence alignment data from IMGTHLA and convert the data into convenient R matrices ready for downstream analysis.
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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, TAP http://opig.stats.ox.ac.uk/resources