immunogenomics

Annotation of mutated peptide sequences with published or novel potential neoantigen descriptors

🌾 Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.

Comparison of gene usage in immune repertoires under different biological conditions

R function to generate a circos-style ggplot from single-cell TCR data.

scLASER: Single-Cell Longitudinal Simulation and Time-Dependent Association Detection

The disTIL immunoprofiling toolkit

QC dashboard that polls vendor SQL Server databases for Luminex bead assay results, computes QC metrics (MFI, bead counts, controls, signal-to-noise), checks thresholds, and charts longitudinal trends in real time.

Allele-specific analysis of the HLA genes

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 Zhang, Wei, Slowikowski, Fonseka, Rao, et al, Nature Immunology, 2019. Single-cell transcriptomics and proteomics data analysis and integration for rheumatoid arthritis synovial tissue. These integrative strategies can be generalized to any other diseases.

Targeted Whole Exome Sequencing (WES) pipeline isolating and functionally classifying structural somatic/germline variants across the Drosophila melanogaster Toll and Relish/IMD innate immune pathways.

Immunogenomics benchmark + skillset for AI agents