immunogenomics/RA_ATAC_multiome

Stars
1
Language
Jupyter Notebook
License
GNU General Publi...
Created over 1 year ago
Updated 5 months ago

immunogenomics/RA_ATAC_multiome

immunogenomics

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

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

harmony

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

presto

Fast Wilcoxon and auROC

Jupyter Notebook

symphony

Efficient and precise single-cell reference atlas mapping with Symphony

Jupyter Notebook

SCENT

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

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"

Jupyter Notebook

LISI

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

HLA-TAPAS

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

Jupyter Notebook

cna

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

amp_phase1_ra

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

Jupyter Notebook

IMPACT

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

scHLApers

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

Jupyter Notebook

singlecellmethods

Collection of useful methods for single cell analysis

Jupyter Notebook

masc

MASC: Mixed-effects Association testing for Single Cells

cdr3-QTL

Trans-association between HLA and TCR-CDR3

sceQTL

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

starCAT

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

Jupyter Notebook

goshifter

TiRP

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

Jupyter Notebook

RA_Atlas_CITEseq

RA Synovial Single-cell Multimodal Cell Atlas

Jupyter Notebook

cov-ldsc

harmony2019

Reproduce analyses in Harmony Manuscript

Jupyter Notebook

RA_GWAS

Trans-ancestry GWAS of rheumatoid arthritis

Jupyter Notebook

tcrpheno

notch

Code to reproduce analyses and figures for manuscript: "Synovial fibroblast positional identity controlled by inductive Notch signaling underlies pathologic damage in inflammatory arthritis"

Jupyter Notebook

FibroblastAtlas2022

Jupyter Notebook

TCAT_analysis

Code repository for TCAT analyses

Jupyter Notebook

sc-h2

Jupyter Notebook

scpost

Implementation of the scPOST framework for simulating single-cell datasets

inflamedtissue_covid19_reference

🧬 Single-cell macrophage integration from inflammatory disease tissues and COVID-19

Jupyter Notebook

TB_Tcell_CITEseq

Code for analysis of memory T cell CITE-seq data

deeplearning_fan

🖥️ Implement deep learning methods in the single-cell world.

GeNA

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

Jupyter Notebook

GPROB

Function to calculate the probability for each of multiple diseases based on a person's genetic profile

itcviewer

🌈 Innate T Cell RNA-seq data viewer.

fibroblastatlas

The Fibroblast Atlas

hla2023

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

Jupyter Notebook

cna-display

Generation of display items for CNA paper

Jupyter Notebook

ra_ipf_cellatlas

Visualize multiple lung phenotypes (RA-ILD, IPF, other) by single-cell

symphony_reproducibility

Jupyter Notebook

amp_phase1_ra_viewer

🌻 View single-cell RNA-seq and mass cytometry data in synovial tissues from patients with RA or OA.

FibroblastAtlas2021

Code to reproduce analyses and figures in 2021 Fibroblast Atlas paper

Jupyter Notebook

TB_progression_GWAS

Codes/data for reproducing figures presented in the TB progression manuscript

dynamicASE

PAUSE_eQTL

Code for dynamic eQTL analysis of PAUSE trial

scpower

single cell power analysis

Jupyter Notebook

harmjan

melody

gene correction stuff

Jupyter Notebook

summerofcode

Resources for Summer of Code '19

Jupyter Notebook

TteK

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

Jupyter Notebook

GeNA-applied

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

Jupyter Notebook

minecraft-seq

Code for analysis of MINECRAFT-seq data

Jupyter Notebook