Raychaudhuri Lab

harmony

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

presto

Fast Wilcoxon and auROC

symphony

Efficient and precise single-cell reference atlas mapping with Symphony

cna

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

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"

SCENT

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

IMPACT

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

scHLApers

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

cdr3-QTL

Trans-association between HLA and TCR-CDR3

singlecellmethods

Collection of useful methods for single cell analysis

sceQTL

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

TiRP

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

cov-ldsc

RA_Atlas_CITEseq

RA Synovial Single-cell Multimodal Cell Atlas

RA_GWAS

Trans-ancestry GWAS of rheumatoid arthritis

tcrpheno

FibroblastAtlas2022

GeNA

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

hla2023

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

sc-h2

GeNA-applied

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

PAUSE_eQTL

Code for dynamic eQTL analysis of PAUSE trial

RA_ATAC_multiome

Code corresponding to Weinand*, Sakaue* et al., The Chromatin Landscape of Pathogenic Transcriptional Cell States in Rheumatoid Arthritis, In Prep., 2023

TteK

TteK (Granzyme K+ CD8 T cells): the core population of inflamed human tissue-associated CD8 T cells

reQTL

Mapping of response eQTL in single cells

1K1K_QC

Additional quality control applied to the published OneK1K dataset

minecraft-seq

Code for analysis of MINECRAFT-seq data

mod-cna

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

tcrpheno_analysis

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