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
- You can install Alleloscope with the code below:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true") install.packages("devtools") devtools::install_github("seasoncloud/Alleloscope") # install library(Alleloscope) # load
You can download example datasets for Alleloscope with the following command:
Using terminal, download the repository.
git clone https://github.com/seasoncloud/Alleloscope.git
- We have included example data in the folder data-raw/.
Detailed tutorials with example datasets
- Click the links below to read detailed tutorials for different data types.
Wu, C.-Y. et al. Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer. Nature Biotechnology (2021): https://doi.org/10.1038/s41587-021-00911-w