Chi-Yun Wu, Zhang Lab, University of Pennsylvania


Alleloscope is a method for allele-specific copy number estimation that can be applied to single cell DNA and ATAC sequencing data (separately or in combination). Allele-specific estimation allows for the more accurate delineation of copy number states and the detection of subclonal copy-neutral loss-of-heterozygosity and mirrored CNA events. On scATAC-seq data, Alleloscope allows integrative multi-omic analysis of allele-specific copy number and chromatin accessibility for the same cell.

For more information about the method, please check out the paper.

Overview of Alleloscope genotyping algorithm

Alt text


devtools::install_github("seasoncloud/Alleloscope") # install
library(Alleloscope) # load

Using terminal, download the repository.

git clone

Detailed tutorials with example datasets


Wu, C.-Y. et al. Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nature Biotechnology (2021):

seasoncloud/Alleloscope documentation built on Feb. 21, 2022, 9:57 a.m.