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/run-rasqual
liangyy/mixqtl
Total and allele specific read based cis-QTL, fine-mapping, and prediction
liangyy/finemapAim
liangyy/encode_ccre_extractor
liangyy/run-aim
Run AIM
liangyy/covid19-wicd-genetics
What I can do with covid-19 genetics?
liangyy/cnn_graph
Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering
liangyy/predixcan_simulator
Simulate phenotype under predixcan model
liangyy/predixcan_prediction
liangyy/process-geuvadis-mixqtl
Repository to process GEUVADIS data for mixQTL example
liangyy/fasterscale
Tutorial for making my first R package by Peter.
liangyy/gene-graph-conv
Towards Gene Expression Convolutions using Gene Interaction Graphs
liangyy/toy-example-of-hail-using-1kg
This repository simulate fake phenotype data for 1000G data using hail.
liangyy/silver-standard-performance
A light and flexible R package to evaluate GWAS-based gene prioritization methods for complex traits.
liangyy/cowplot
cowplot: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
liangyy/PrediXcan
PrediXcan Project
liangyy/gtex-pipeline
GTEx & TOPMed data production and analysis pipelines
liangyy/ggmix
liangyy/phaser
phasing and Allele Specific Expression from RNA-seq
liangyy/ggsb-jc-2019
This repository is for presenting in GGSB journal club in 2019 @ UChicago
liangyy/WASP
WASP: allele-specific pipeline for unbiased read mapping and molecular QTL discovery
liangyy/learn-japanese
liangyy/explore-eqtl
The repository for rotation project at Matthew's lab. See results at
liangyy/rasqual
Robust Allele Specific Quantification and quality controL
liangyy/notebook
Keep note along with thoughts
liangyy/deep_variant_annotation
This is a light and easy-to-use version of deep_variant for annotate a list of variant using model trained by deep_variant
liangyy/footprint_annotation
See results here
liangyy/deep_variant
Explore functional effect of non-coding variant using deep learning
liangyy/phenotype-epistasis
This repository is for the project on discovering the genetic background effect of complex trait on the basis of domain knowledge
liangyy/fiveMinuteStats
A repo of short "vignettes" illustrating statistical concepts