T/B cell receptor sequencing analysis notes

• 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. installation is very hard. 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

• CellaRepertorium

• migec:A RepSeq processing swiss-knife.

• MiXCR is a universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data.

• tcR: an R package for T cell receptor repertoire advanced data analysis

• ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

• Grouping of Lymphocyte Interactions by Paratope Hotspots paper: https://www.nature.com/nature/journal/v547/n7661/full/nature22976.html

• 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

• scirpy: A scanpy extension for single-cell TCR analysis.

• 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.

• 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).

• TCRdb A comprehensive database of human T-cell receptor (TCR) sequences

• Immuno-Navigator A database for gene coexpression in the immune system