Pinned Repositories
genomewide_annotation
Given a bed file, annotate each position of the given regions in allele-specific manner (but not strand-specific) and generate TSV file. For further usage, it also provides scripts to convert TSV to BED by applying some customized filtering rules.
gwas-abc
ldpred
ldpred in python3
misc-tools
A scripting gallery containing random this and that.
mixqtl
Total and allele specific read based cis-QTL, fine-mapping, and prediction
mixqtl-pipeline
This repository contains pipeline to prepare input files for mixQTL
ptrs-tf
Building PTRS model using TensorFlow
silver-standard-performance
A light and flexible R package to evaluate GWAS-based gene prioritization methods for complex traits.
template_r_documentation
This is a light template for documentation based on rmarkdown
ukb_idp_genetic_arch
liangyy's Repositories
liangyy/misc-tools
A scripting gallery containing random this and that.
liangyy/template_r_documentation
This is a light template for documentation based on rmarkdown
liangyy/ukb_idp_genetic_arch
liangyy/gwas-abc
liangyy/mixqtl-pipeline
This repository contains pipeline to prepare input files for mixQTL
liangyy/ptrs-tf
Building PTRS model using TensorFlow
liangyy/ptrs-ukb
Calculate PTRS for UKB data
liangyy/SPrediXcan2PTRS
liangyy/brainxcan-docs
liangyy/mixqtl-gtex
mixQTL pipeline for GTEx v8 data
liangyy/brainxcan
liangyy/ebnm
R package to fit Empirical Bayes Normal Means model.
liangyy/flashr
R package for Empirical Bayes Factor Analysis.
liangyy/gcta
GCTA software
liangyy/haplotype-po
Imputing the parent of origin of haplotype
liangyy/idea-playground
Play with thoughts
liangyy/journal-club
Short summaries of articles & discussions by UCHG Computational Biology Group
liangyy/lassosum
LASSO for GWAS with summary statistics
liangyy/lc-notebook
LeetCode NoteBook
liangyy/ldsc
LD Score Regression (LDSC)
liangyy/learn-torch-geometric
liangyy/MetaXcan
MetaXcan software and manuscript
liangyy/ml-notebook
liangyy/nextflow-vim
Nextflow plugin for VIM
liangyy/ptrs-graph
liangyy/snpnet
snpnet: Fast and scalable lasso/elastic-net solver for large SNP data
liangyy/summary-gwas-imputation
harmonization, liftover, and imputation of summary statistics from GWAS
liangyy/susieR
an R package for "sum of single effects" regression
liangyy/tensorqtl
Ultrafast GPU-based QTL mapper
liangyy/transethnic_prs