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Stars

Genetic

Genetic analysis tools
38 repositories

LD Score Regression (LDSC)

Python 666 348 Updated Aug 16, 2024

A flexible tool for the multi-resolution localization of causal variants across the genome, accounting for population structure.

C++ 14 Updated Jul 7, 2022

MsCAVIAR identifies causal variants using GWAS summary statistics from multiple studies, e.g. trans-ethnic fine mapping

C++ 6 3 Updated Nov 4, 2021

RFMIX - Local Ancestry and Admixture Inference Version 2

C++ 81 24 Updated Dec 12, 2022

Official code repository for GATK versions 4 and up

Java 1,746 596 Updated Jan 15, 2025

A simple way to update kgp IDs from the Illumina-Human Omni 2.5M array to rs IDs.

6 1 Updated Aug 14, 2017

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

237 59 Updated Nov 28, 2022

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

JavaScript 156 29 Updated Mar 15, 2023

Meta analysis using explicit covariance matrix

R 5 Updated Apr 20, 2020

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)

Python 177 55 Updated Jul 6, 2023

R-package for structural equation modeling based on GWAS summary data

R 215 56 Updated Dec 19, 2024

tools for adding mutations to existing .bam files, used for testing mutation callers

Python 238 86 Updated Oct 18, 2024

Stratified squared trans-ethnic genetic correlation

JavaScript 12 2 Updated May 12, 2022
R 56 9 Updated Jul 1, 2024

Performant Pythonic GenomicRanges

Python 448 46 Updated Jun 4, 2024

An R package for performing association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using STAARpipeline

R 61 20 Updated Dec 29, 2024

tomato graph pangenome

Python 76 18 Updated Dec 13, 2022

An R package for multivariate adaptive shrinkage.

R 91 19 Updated Nov 7, 2024

Human reference genome analysis sets

Makefile 50 3 Updated Jun 17, 2023

The complete sequence of a human genome

934 99 Updated Nov 19, 2024

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

mupad 94 15 Updated May 21, 2024

Contamination from Homozygous Alternate Reference Reads

Python 8 2 Updated Oct 31, 2023

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Python 3,293 732 Updated Dec 9, 2024

multi_tbx: a simple tool for indexing VCF files and extract variant records for variant data stored in multiple VCF files.

Rust 10 1 Updated Jan 7, 2022

Program for analysing NGS data.

C++ 231 51 Updated Nov 14, 2024

Repository for code to produce phased 1000 Genomes Project haplotypes called against the CHM13v2 T2T reference genome.

Shell 10 Updated Oct 31, 2024

📮 A Memory-efficient, Visualization-enhanced, and Parallel-accelerated Tool For Genome-Wide Association Study

R 284 72 Updated Jan 13, 2025

📊 Circular and Rectangular Manhattan Plot

R 543 114 Updated May 20, 2024

Biological sequence analysis for the modern age.

Python 205 12 Updated Dec 17, 2024