Skip Navigation
Increase font size
Decrease font size

Li Group Software

The following software packages and utilities can be downloaded freely. If you find them useful, please email me: Comments and suggestions are welcome!

Software    Database    Utilities   


  • AbCD Arbitrary Coverage Design for Sequencing-based Studies
  • BETASEQ Data Correction in Unbalanced Sequencing Studies for Valid Rare Variant Association Testing
  • CUE CpG impUtation Ensemble for DNA Methylation Levels Across the HumanMethylation450 (HM450) BeadChip and HumanMethylation EPIC (HM850) BeadChip Platforms
  • EMLRT Post-Imputation Association Analysis using EM Likelihood Ratio Tests (LRT)
  • DISSCO Direct Imputation of Summary Statistics allowing COvariates
  • eSCAN Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data
  • FastHiC A Fast Algorithm to Detect Long-Range Chromosomal Interactions from Hi-C Data
  • FIREcaller an R package for detecting frequently interacting regions from Hi-C data
  • HiC-ACT An aggregated Cauchy test (ACT) based approach to detect long-range chromatin interactions in Hi-C Data
  • HMRFBayes A Hidden Markov Random Field Based Bayesian Method For the Detection of Long-range Chromatin Interactions in Hi-C Data
  • HPRep A methodological framework to quantify reproducibility between PLAC-Seq or HiChIP datasets
  • HUGIN Hi-C Unifying Genomic INterrogator - Web-based viewer of Hi-C across 21 different cells and tissue data with genomic information
  • iSMNN Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement KARMA K-tuple Alignment with Rapid Matching Algorithm -->
  • LocusXcanR an R Shiny application to interactively visualize TWAS results
  • MaCH MArkov Chain Haplotyping: rapid haplotyping and genotype imputation (wiki)
  • MaCH-Admix Genotype Imputation for Admixed Populations or with Large Reference Panels
  • mach2dat Imputation-based analysis of binary traits (windows version) (How-To-Use-The-Windows-Command-Line)
  • mach2qtl Imputation-based analysis of quantitative traits (windows version) (How-To-Use-The-Windows-Command-Line)
  • MUNIn Multiple tissue UNifying long-range chromatin Interaction detector
  • SAFE-clustering Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
  • SAME-clustering Single-cell RNA-seq Aggregated Clustering via Mixture model Ensemble
  • ShotGun a flexible short read simulator
  • SMNN Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection
  • SMUT and gSMUT R Package for Testing the Mediation Effect of Multiple SNPs on an Outcome Through a Mediator
  • thunder LD-based genotype caller and haplotyper on massively parallel sequencing data (wiki)
  • TOP-LD a tool to explore linkage disequilibrium (LD) using TOPMed whole genome sequence (WGS) data
  • UNCcombo Likelihood based association testing for next generation sequencing data without intermediate genotype calling
  • TWO-SIGMA and TWO-SIGMA-G Differential expression (DE) analysis and gene set testing (GST) in single-cell RNA-seq data
  • VAMPIRE R Shiny application: Variant Annotation Method Pointing to Interesting Regulatory Effects
  • WHaIT Weighted Haplotype and Imputation dosage Tests for rare variants association



  • CalcMatch Concordance between two sets of genotype data (wiki)
  • changePedStrand Change Strand (by base pairing) for a Pedigree file
  • Concatenate Haplotypes Concatenate Two Sets of Haplotypes
  • doseR2 Dosage r2 Calculator for MaCH input (old version)
  • doseR2_VCF(beta) Dosage r2 Calculator for VCF input (beta version)
  • dose2geno Generate Best Guess Genotypes from Dosage and Info File
  • ExtractImputed Extract information for a subset of sites from imputed dataset
  • flipDosages Flip Dosages (to obtain consistent AL1/AL2 coding across multiple dosage files)
  • Convert genotypes (in .ped format) to haplotypes
  • Convert haplotypes to genotypes (in .ped format)
  • Extract haplotypes for a subset of markers
  • haploxt LD Calculator from Phased Haplotypes (wiki)
  • Ligate Haplotypes Ligate Haplotypes with Two Overlapping Regions
  • prob2dose Converts MaCH/MaCH-admix prob output to MaCH/MaCH-admix dose output
  • prob2plink Converts MaCH/MaCH-admix prob+info output to PLINK dosage file
  • ped2numeric Convert QTDT pedigree file into 012 coding (dosage) file
  • r2_hat Calculate Imputation Quality Estimate (r2_hat) from dosage data
  • r2_hat_VCF(beta) A new version of r2_hat, taking VCF as input and supporting sample exclusion when calculating r2_hat
  • RegionalHapMapExtractor Extract a Region from HapMapII for MaCH/MaCH-admix imputation
  • splitPed Splits a pedigree file into smaller files with subsets of markers (wiki)
  • splitRef Splits a reference haplotype file into smaller files with subsets of markers (wiki)
  • TOPMed5bImputation Imputation and Post-imputation Quality Evaluation