Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

simplified cellranger for long-read data

catELMo: Context-Aware Amino Acid Embedding Advances Analysis of TCR-Epitope Interactions

Highly informative TCR representation model

A database of T-cell receptor sequences

Comparison of gene usage in immune repertoires under different biological conditions

R package. Main goals are to fit models to the clone size distribution of the TCR repertoire, and to perform model-based comparative analysis of samples.

Scripts related to bulkRNA-seq as well as single-cell CITE-seq and VDJ-seq data of Gearty et al. (2021)

TCRscape - a tool for simultaneous multimodal gene expression and clonotype analysis of single T-cells profiled via the BD Rhapsody system.

An example of immunopipe

[UNDER DEVELOPMENT] Pipeline for mapping and annotating T- and B-cell receptor gene rearrangement sequences

Analysis functions for deep sequenced immune repertoire (Repseq) datasets in R

MiXCR Clonotyping Block

Deep unsupervised learning methods for the identification and characterization of TCR specificity to Sars-Cov-2

Dynamics of peripheral T-cell repertoire in pediatric cancer patients over the course of chemoradiation

Shiny App that interfaces with TCRDist3

Multimodal immunogenomic biomarker analysis of tumours from pediatric patients enrolled to a phase 1-2 study of single-agent atezolizumab

Scripts used in the manuscript titled "Autoimmunity to hypocretin and molecular mimicry to flu in Type 1 narcolepsy"