Discover immunogenomics/singlecellmethods Open Source project

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Created almost 6 years ago
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immunogenomics

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Collection of useful methods for single cell analysis

harmony

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

512

presto

Fast Wilcoxon and auROC

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148

symphony

Efficient and precise single-cell reference atlas mapping with Symphony

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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.

Python

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

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masc

MASC: Mixed-effects Association testing for Single Cells

cdr3-QTL

Trans-association between HLA and TCR-CDR3

HTML

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

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goshifter

GoShifter

Python

TiRP

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

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RA_Atlas_CITEseq

RA Synovial Single-cell Multimodal Cell Atlas

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cov-ldsc

Python

harmony2019

Reproduce analyses in Harmony Manuscript

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RA_GWAS

Trans-ancestry GWAS of rheumatoid arthritis

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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"

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FibroblastAtlas2022

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TCAT_analysis

Code repository for TCAT analyses

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sc-h2

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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.

HTML

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

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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

RA_ATAC_multiome

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

Jupyter Notebook

PAUSE_eQTL

Code for dynamic eQTL analysis of PAUSE trial

scpower

single cell power analysis

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harmjan

Java

melody

gene correction stuff

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summerofcode

Resources for Summer of Code '19

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TteK

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

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GeNA-applied

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

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minecraft-seq

Code for analysis of MINECRAFT-seq data

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immunogenomics/singlecellmethods

immunogenomics

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