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117 public repositories
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🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires from any type of sequencing data. Free for academic use only.
Updated
Sep 18, 2021
Java
🗂️ Git-based TCR database storage & management. Submissions welcome!
Updated
Mar 30, 2022
Groovy
Post-analysis of immune repertoire sequencing data
Updated
Mar 9, 2022
Groovy
Tools and databases for analyzing HLA and VDJ genes.
Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
Updated
Apr 29, 2022
Jupyter Notebook
An interactive web portal for exploring immuno-oncology data
IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
HTS-compatible wrapper for IgBlast V-(D)-J mapping tool
Updated
Mar 2, 2018
Groovy
A RepSeq processing swiss-knife
Updated
Mar 11, 2022
Groovy
[DEPRECATED, see
https://immunarch.com/ ] tcR: an R package for immune receptor repertoire advanced data analysis.
Python package and command line tool for epitope prediction
Updated
Mar 17, 2021
Jupyter Notebook
Precision HLA typing from next-generation sequencing data
Updated
Mar 24, 2022
Nextflow
simpler single cell RNAseq data clustering
An R Interface to the ImmuneSpace database portal
⚙️ A lightweight immune repertoire browser
Updated
Dec 10, 2019
JavaScript
Stitchr - a Python script to stitch together coding TCR nucleotide sequences from V, J, and CDR3 info
Updated
Apr 27, 2022
Python
Huge-scale, high-performance flow cytometry clustering in Julia
Updated
Apr 8, 2022
Julia
A data-centric flow/mass cytometry automated analysis framework
Updated
Feb 16, 2022
Python
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Immunology Informatics - Big Data Analysis in Immunology - Tutorials
ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
Updated
Dec 12, 2021
Python
An R package to analyze single-cell V(D)J data
Comparison of Adaptive Immune Receptor Repertoires
Updated
Apr 16, 2022
Python
📝 [Tutorial] RepSeq data mining basics in R
AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation
Updated
May 4, 2022
Jupyter Notebook
Code for Celia and Nils' immune aging project.
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I removed several headings that had been added early on in brainstorming for this manuscript. If anyone is looking for ideas of how to contribute, you could definitely look into how these drug development strategies are being applied to COVID-19!
Additionally, here is the template for adding in