MiXCR Clonotyping Block

Simple Contrastive Embedding of the Primary sequence of T cell Receptors

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

simplified cellranger for long-read data

Will be used for my first formal research undertaking as a student of Computer Science and Statistics

An example of immunopipe

analysis of antibody diversity, .wdl wrapper workflow

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

Comparison of gene usage in immune repertoires under different biological conditions

🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

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

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

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

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

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

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

📑 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.

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

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

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.