whereAreECDNAs

whereAreECDNAs is an R package designed to identify ecDNA-positive cells from single-cell ATAC-seq data.

The package uses chromatin accessibility signals within predefined ecDNA amplicon intervals to estimate the likelihood that individual cells harbor ecDNA.

Installation

The package can be installed directly from GitHub using devtools:

install.packages("devtools")
library(devtools)

install_github("LupienLab/whereAreECDNAs")

Alternatively, using remotes:

install.packages("remotes")

remotes::install_github("LupienLab/whereAreECDNAs")

After installation, load the package with:

library(whereAreECDNAs)

Usage

A complete example workflow is provided in the testDemo.R script included in the repository. Before running the script, update the input file paths and analysis parameters according to your dataset.

Input Data

The analysis generally requires:

• A single-cell ATAC-seq fragment file.
• A list of valid cell barcodes.
• Genomic coordinates defining the ecDNA amplicon intervals.

All genomic coordinates should use the same reference genome assembly, such as hg38.

Output

whereAreECDNAs generates cell-level results describing:

• The estimated ecDNA content of individual cells.
• The probability that each cell is ecDNA-positive.
• A binary ecDNA-positive or -negative classification for each cell.

These outputs can be integrated with cell-type annotations, malignant cell classifications, transcriptional states, copy-number profiles, or other single-cell metadata for downstream analyses.

Issues and Support

Questions, bug reports, and feature requests can be submitted through the GitHub Issues page:

https://github.com/LupienLab/whereAreECDNAs/issues

When reporting an issue, please include:

• The R version.
• The package version or GitHub commit.
• A minimal reproducible example.
• The complete error message.
• Relevant session information generated using: sessionInfo()

License

Please refer to the LICENSE file in the repository for licensing information.