LongcallR is a SNP caller for single molecule long-read RNA-seq data

Allele-specific alignment sorting

Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

Mixture Models for Allelic Imbalance Estimation

WASP2: High-performance allele-specific analysis pipeline for next-generation sequencing data

early version of (Pipeline for detection of differential allelic imbalance from RNA-seq)

C++ Implementation of EMASE

Single Cell Allele-Specific Analysis - Containerized tool for genotyping, phasing, mapping bias correction, and generation of single cell allele-specific counts

Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

Haplotype-Assisted Read Parsing

PARamrfinder is a high performance parallel tool to predict allele-specific DNA methylation (ASM) in mammals in the absence of SNP data.

R scripts to process input/output related to GeneiASE software

Allele-specific RNA-seq pipeline: STAR + SNPsplit + featureCounts (Nextflow DSL2)

Supplementary Materials for "Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)"

Tools to analyse allele-specific methylation using bisulfite sequencing data