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)

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

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

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

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

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

Shiny App that interfaces with TCRDist3

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

analysis of antibody diversity, .wdl wrapper workflow

📑 A library of example code -aka cheatsheets- for tools I use or analyses I carry out pretty often. This repo doubles as an easy way to find the code I need without going through all my scripts.

Code for Jonsson*, Zhang*, et al, TteK (Granzyme K+ CD8 T cells), Science Translational Medicine, 2022: the core population of inflamed human tissue-associated CD8 T cells.

scRNA-seq for COVID-19 samples, with healthy controls.

Code for HRDetect, image analysis, TCR - seq from HGSOC samples

A brief analysis of donor diversity in publicly available T cell receptor (TCR) data.

TCR clonotype analysis using mixcr and immunarch.