Pinned Repositories
AdmixSim2
forward-time simulator of population genetic data
ArchaicSeeker2.0
ArchaicSeeker is a series of software for detecting archaic introgression sequences and reconstructing introgression history. The latest version of this series, ArchaicSeeker 2.0, has the following three notable improvements compared with the original version of this software. First, it can automatically determine the boundary of each introgressed sequence. Next, it is capable of tracing both known and unknown ancestral sources of a given introgressed sequence. Finally, it has the ability to reconstruct the introgression history with more sophisticated introgression models.
Chinese-Pangenome-Consortium-Phase-I
CPC-graph-based-NGS-pipeline
A graph-based pipeline used to call/genotype snvs/indels/SVs from NGS data
MultiWaver2.0
MultiWaver series software was designed to infer population admixture history in case of various and complex scenarios. The earlier version of MultiWaver considered only the discrete admixture models. In the newly developed version MultiWaver 2.0, we implemented a more flexible framework to automatically select an optimal admixture model among discrete models and continuous models.
NGS.PRSS1-2caller
NGS.PRSS1-2caller is a toolkit for calling genetic variants at PRSS1-PRSS2 locus, which enables detecting SNV, INDEL and CNV with high accuracy and sensitivity.
PanGenome_VCF_PostProcess
A simple pipeline to process the VCF deconstructed from the VG pangenome graph
PGGSVpipeline
Theta_D_H.Est
Calculator for statictics including Theta, D, H, and so on, based on the VCF input.
Y-LineageTracker
A high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Shuhua-Group's Repositories
Shuhua-Group/Y-LineageTracker
A high-throughput analysis framework for Y-chromosomal next-generation sequencing data
Shuhua-Group/ASEkit
A tool applied to detect allelic expression sites
Shuhua-Group/ADMIXTURE.merge
To merge the replicates of ADMIXTURE analysis and provide summary report.
Shuhua-Group/AdmixSim
Java Version for the AdmixSim: A Forward-Time Simulator for Various and Complex Scenarios of Population Admixture
Shuhua-Group/AncestryPainter
AncestryPainter is a graphic program used to illuminate the ancestry compositions of populations and individuals.
Shuhua-Group/CVETool
Composite variant expression tool
Shuhua-Group/CAMer
Continuous Admixture Modeler: R package for Continuous Admixture Modeling (CAMer)
Shuhua-Group/PEAS
Package for Elementary Analysis for SNP data
Shuhua-Group/The_First_Repository
Some examples about using GitHub
Shuhua-Group/WinXPCNVer
WinXPCNVer is tool package for calculating the Vst values between two populations probe by probe in a sliding window, which could be used to detect highly differentiated variants between populations.
Shuhua-Group/ArchaicSeeker
ArchaicSeeker is a software to detect archaic-like haplotypes in non-African modern human.