Most of my software as well as vignettes and scripts for the analyses connnected to my research can be found on my GitHub page. I maintain the following software packages:

Monopogen (Single nucleotide variant calling from single cell sequencing)

Monopogen is developed to achieve SNV calling from single cell RNA sequencing, single cell ATAC sequencing. The package Monopogen is available from GitHub

BindSC (Bi-order integration of single cell multi-omics data)

This tool is developed to achive bi-order integration (in silico multi-omics data) of single cell RNA sequencing, single cell ATAC sequencing, spacial transcriptomics and CyTOF data. The package BindSC is available from GitHub

WEScall (A genotype calling pipeline for whole exome sequencing (WES) data)

WESCall can analyze both target and off-target data, and is a useful tool to facilitate WES sutides with decent amount of off-target data.The package WEScall is available from GitHub

SEEKIN (Sequencing-based estimation of kniship and inbreeding coefficients)

This program estimates the kinship and inbreeding coefficients based on extremely low-sequencing coverage datasets (typically lower than 0.5X). The code is available from GitHub.

AMMO (An integrated package for whole-genome restriction mapping and genome scaffolding)

This is an integrated program that generates 2b-RAD-based restriction maps for scaffolding draft genome assemblies produced by using short Illumina reads or long PacBio reads. The package AMMO is available from GitHub

RADTyping (De novo RAD Genotyping in Mapping Populations)

This is an integrated package for accurate De Novo codominant and dominant RAD genotyping in mapping populations. The code is available from GitHub.