Kai(kevin) Luo's repositories
awesome-multi-omics
List of software packages for multi-omics analysis
ADRD_Brain_Aging
ADRD Brain Aging projects
analysis_pipeline_WDL
Collection of WDL workflows based off the University of Washington TOPMed DCC Best Practices for GWAS. The WDL structure was based upon CWLs written by the Seven Bridges development team.
bigsnpr
R package for the analysis of massive SNP arrays.
Blogdown
RBlogdown
formatbook
A collection of commonly used format for quick lookup.
GenomicSEM
R-package for structural equation modeling based on GWAS summary data
gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
gwaslab
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
hail
Cloud-native genomic dataframes and batch computing
INF
SCALLOP-INF analysis
Lifelines_NEXT
Lifelines NEXT is a birth cohort designed to study the effects of intrinsic and extrinsic determinants on health and disease in a four-generation design. It is embedded within the Lifelines cohort study, a prospective three-generation population-based cohort study recording the health and health-related aspects of 167,729 individuals living in Nort
mdd-proteome-ancestry
Group 6 project
mlexperiments
An extensible framework for reproducible machine learning experiments
nestedcv
Nested cross-validation with feature selection filters
package-BoutrosLab-plotting-general
Functions to Create Publication-Quality Plots
pgsc_calc
The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation
prop-coloc
A summary data-based proportional colocalization test that accounts for uncertainty in variant selection
ranger
A Fast Implementation of Random Forests
scDRS
Single-cell disease relevance score (scDRS)
survex
Explainable Machine Learning in Survival Analysis
systemsgenetics
Generic Java genotype reader / writer, QTL mapping software, Strand alignment tool
TCSC
TCSC (Tissue co-regulation score regression) is a statistical genetics method to identify causal tissues in diseases and complex traits.
treeshap
Explain your tree model with shap values efficiently
TWAS-GSEA
R script that performs gene-set or gene property analysis using TWAS results.
UKB_RAP
Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.