immunology

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.

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

📚 Tools and databases for analyzing HLA and VDJ genes.

A collaborative review of the emerging COVID-19 literature. Join the chat here:

🗂️ Git-based TCR database storage & management. Submissions welcome!

Post-analysis of immune repertoire sequencing data

A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces

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

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:

An interactive web portal for exploring immuno-oncology data. This repo now superseded by iatlas-app

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Python package and command line tool for epitope prediction

A RepSeq processing swiss-knife

Precision HLA typing from next-generation sequencing data

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.

Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info

simpler single cell RNAseq data clustering

A data-centric flow/mass cytometry automated analysis framework

R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations