Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.

Bulk ATAC-seq data of tumour samples result in an averaged signal across different cell-types (cancer, stromal, vascular and immune cells). We propose a deconvolution framework called EPIC-ATAC, which relies on newly identified cell-type specific ATAC-Seq marker peaks and reference profiles for all major cancer-relevant cell-types to predict the proportions of each cell-type.

To evaluate EPIC-ATAC, we generated a newly generated bulk ATAC-Seq dataset from peripheral blood mononuclear cells (PBMCs) samples, from which the number of cells in each cell-type has been estimated using flow cytometry, as ground truth for cell proportions. The data provided in this Zenodo deposit correspond to:

- The raw counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts.txt

- The normalized (TPM-like) counts matrix for each peak called in this ATAC-Seq dataset: PBMC_counts_norm.txt

- The cell fractions of each cell type in each sample: PBMC_cell_fractions.txt

- The peaks called in each sample using MACS2 (*narrow.peaks): *_normalized.narrowPeak

- Bed files listing ATAC-Seq fragments for each sample: *.bed

We also evaluated EPIC-ATAC on multiple pseudobulks generated from single-cell ATAC-Seq data. We provide here rds files containing the pseudobulk data used in our work for the evaluation of EPIC-ATAC.