README.md

In seasoncloud/Alleloscope: Allele-specific copy number genotyping for single cell sequencing data

Alleloscope

Chi-Yun Wu, Zhang Lab, University of Pennsylvania

Description

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

Install

• 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.

• scDNA-seq

• scDNA-seq with 2nd-stage estimation
• scATAC-seq
• Matched scDNA-seq and scATAC-seq

Citation

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

seasoncloud/Alleloscope documentation built on March 17, 2023, 1:14 a.m.