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63_immune_cells

Gene expression profiles of 63 immune cell types

co_expression_pattern.r

eas_partitioned_ldscore

Partitioned LD Scores for the EAS population

fangli359.github.io

genopred

Genotype-based Prediction (GenoPred)

gsa.tissue.celltype.enrich

Repository containing source code, data, etc necessary to run Gene Set Analysis, Celltyping using MAGMA/Celltyping and Tissue Enrichment Analysis. Some of the formulas have been adapted from: NathanSkene/ALS_Human_EWCE, neurogenomics/EWCE, NathanSkene/MAGMA_Celltyping and jbryois/scRNA_disease github repositories.

gwas_ukbb_regenie

Running GWAS on Kidney's latent phenotypes via REGENIE v.2.1

hdl

High-definition likelihood inference of genetic correlations (HDL)

hyprcoloc

R package for performing high dimensional multi-trait colocalization analyses using GWAS summary data

jm-gwas

GWAS pipeline: Vitamin-D in the UKB including SMR analysis

kidneygwas1

ldsc

LD Score Regression (LDSC)

ldsc_nf

partitioned LDSC pipeline with nextflow

locuscompare

LocusCompare is an interactive visualization tool for comparing two genetic association datasets.

locuscomparer

LocusCompareR is a R package with visualization tools for comparing two genetic association datasets.

magma_celltyping

Find causal cell-types underlying complex trait genetics

moloco

A tool for performing multiple-trait colocalization test using GWAS summary statistics

pheweb

A tool to build multi-phenotype GWAS browsers

proda

Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/

scgwas

A method which leverages scRNA-seq data to achieve two goals: (1) to infer the cell types in which the disease-associated genes manifest and (2) to construct cellular modules which imply disease-specific activation of different processes.

scrna_disease

Code for our paper: https://www.biorxiv.org/content/10.1101/528463v1

single-cell-data-analysis

Mouse Kidney Cell Single-Cell Data Analysis Project

target_discovery_workflow_gwas

Summer 2022 internship project into target discovery for kidney disease through the integration of GWAS and QTL data sources.

wilson_muto_ncomm_2022

Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq