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

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

Simple Contrastive Embedding of the Primary sequence of T cell Receptors

A database of T-cell receptor sequences

Comparison of gene usage in immune repertoires under different biological conditions

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

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.

Slides for presentations by ImmunoMind team

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

An example of immunopipe

MiXCR Clonotyping Block

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

📑 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 of antibody diversity, .wdl wrapper workflow

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.

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