eccDNAscope

eccDNAscope is an R package that provides tools for analyzing and visualizing eccDNA through scATAC data. It includes functions for converting Cell Ranger objects to Seurat objects, performing quality control, identifying eccDNA features, visualizing eccDNA in specific cells, analyzing clone trajectories, conducting shared eccDNA analysis, and more.

Workflow

Overview

eccDNAscope provides users with the following functionalities:

Process Cell Ranger results of scATAC data into an eccDNA object(Seurat object), and complete the processes of dimensionality reduction, clustering, gene activity calculation, and cell annotation. more details
Calculate the number of fragments with copy number amplification, adapter(breakpoint), eccDNA genes in each cell. Plot the distribution of eccDNA genomic regions and Visualizing eccDNA in specific cell. more details
Create a data frame to record the copy number information of each eccDNA-related gene in each cell across all samples and perform clone trajectory analysis. more details
Determin cell lineages by single eccDNA molecules and corroborat by chromatin accessibility similarities. more details

Data Download

In addition, we provide the scATAC-seq and scRNA-seq data of cutaneous squamous cell carcinoma (CSCC) used in this study. You can download it via the following link. more details

Click here to download the scATAC-seq data

Click here to download the scRNA-seq data

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Developers

Jie Li, Rongkai Lv