📑 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

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

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

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

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

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

TCR clonotype analysis using mixcr and immunarch.

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

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

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

MiXCR Clonotyping Block

An example of immunopipe

Slides for presentations by ImmunoMind team

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

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.

Comparison of gene usage in immune repertoires under different biological conditions

A database of T-cell receptor sequences