GPlinksR

Building Gene-Peak Network for ATAC-RNA Integration

Bioconductor version: 3.24 · Package version: 0.99.2

GPlinksR constructs gene-peak regulatory networks for ATAC-RNA integration by combining enhancer-based, promoter-based, and proximity (closest-gene) mappings. The package accepts direct peak and gene vectors as well as container-based inputs through a wrapper for common Bioconductor object classes. Enhancer-gene links are obtained from the PEREGRINE enhancer-gene datasets provided by AnnoQ, while promoter and gene coordinates are retrieved from EnsDb.Hsapiens.v86.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GPlinksR")