Raychaudhuri Lab

amp_phase1_ra

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

cna

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies

HLA_analyses_tutorial

A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"

IMPACT

Code for creating cell-type-specific regulatory element annotation files

LISI

Methods to compute Local Inverse Simpson's Index (LISI)

presto

Fast Wilcoxon and auROC

SCENT

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

symphony

Efficient and precise single-cell reference atlas mapping with Symphony

immunogenomics/harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

immunogenomics/presto

Fast Wilcoxon and auROC

immunogenomics/symphony

Efficient and precise single-cell reference atlas mapping with Symphony

immunogenomics/SCENT

Single-Cell ENhancer Target gene mapping using multimodal data with ATAC + RNA

immunogenomics/HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies

immunogenomics/HLA_analyses_tutorial

A thorough tutorial on HLA imputation and association, accompanying our manuscript "Tutorial: A statistical genetics guide to identifying HLA alleles driving complex disease"

immunogenomics/cna

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

immunogenomics/scHLApers

Code to run the scHLApers pipeline for personalized single-cell HLA quantification

immunogenomics/cdr3-QTL

Trans-association between HLA and TCR-CDR3

immunogenomics/sceQTL

Code for single-cell eQTL analysis of memory T cell data in Nathan, et al. bioRxiv (2021)

immunogenomics/TiRP

code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)

immunogenomics/cov-ldsc

immunogenomics/RA_Atlas_CITEseq

RA Synovial Single-cell Multimodal Cell Atlas

immunogenomics/RA_GWAS

Trans-ancestry GWAS of rheumatoid arthritis

immunogenomics/starCAT

Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs

immunogenomics/tcrpheno

immunogenomics/FibroblastAtlas2022

immunogenomics/sc-h2

immunogenomics/GeNA

Genotype-Neighborhood Associations: A tool for identifying genetic variant associations to the abundance of cell states in single-cell datasets

immunogenomics/hla2023

Code for mapping single-cell eQTLs for HLA genes across four cohorts

immunogenomics/TCAT_analysis

Code repository for TCAT analyses

immunogenomics/GeNA-applied

Code and analyses supporting the GeNA single-cell csaQTL manuscript.

immunogenomics/PAUSE_eQTL

Code for dynamic eQTL analysis of PAUSE trial

immunogenomics/RA_ATAC_multiome

Code corresponding to Weinand et al., The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis, Nature Communications, 2024

immunogenomics/reQTL

Mapping of response eQTL in single cells

immunogenomics/TB-g2g

Code for genome-to-genome study of tuberculosis

immunogenomics/1K1K_QC

Additional quality control applied to the published OneK1K dataset

immunogenomics/minecraft-seq

Code for analysis of MINECRAFT-seq data

immunogenomics/mod-cna

CNA package with the incorporation of modifications to illustrate and address confounding by cell count.

immunogenomics/tcrpheno_analysis

Code for analysis of TCR and T cell state data in Lagattuta, et al. bioRxiv (2023)