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alice

Detecting TCR involved in immune responses from single RepSeq datasets

awesome-vdj

Tools and databases for analyzing HLA and VDJ genes.

decombinator

Decombinator v3: fast, error-correcting analysis of TCR repertoires

deepcat

Deep Learning Method to Identify Cancer Associated TCRs

dysfunction_interaction_test

ggbeeswarm

Column scatter / beeswarm-style plots in ggplot2

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwas

Scripts for GWAS association and metaanalysis

gwas_scripts

Codebook from my GWAS cookbook

immunarch

An R Package for Fast and Effortless Analysis of Large-Scale Immune Repertoire Data

impres-codes

ngscheckmate

Software program for checking sample matching for NGS data

pipelines

RPD Pipelines

r_plot

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

tcr

tcR: an R package for immune receptor repertoire advanced data analysis.

tcr-3d

tcr-annotation-methodology

📝 [Paper/Tutorial] T-cell repertoire annotation and motif discovery

timer

A comprehensive resource for the clinical relevance of tumor-immune infiltrations.

uveitisjia_mhc-finemapping

Scripts and data used in analyses for "An amino acid motif in HLA-DRβ1 distinguishes patients with uveitis in juvenile idiopathic arthritis." Preprint: https://www.biorxiv.org/content/early/2017/08/14/140954

vdjmatch

Matching T-cell repertoire against a database of TCR antigen specificities

vdjtools

Post-analysis of immune repertoire sequencing data