Package: eccDNAscope
Type: Package
Title: Constructing ecDNA through single cell ATAC-seq and Conducting
        Cloning and Expression Studies
Version: 0.1.0
Author: Rongkai Lv
Maintainer: Rongkai Lv <rongkailv@gmail.com>
Description: This package provides tools for analyzing and visualizing ecDNA through scATAC data. It includes functions for converting cellranger objects to Seurat objects, quality control, identifying ecDNA features, clone trajectory analysis, shared ecDNA analysis, and more.
License: MIT + file LICENSE
Encoding: UTF-8
Imports: ape (>= 5.7-1), ChIPseeker (>= 1.42.0), dplyr (>= 1.1.4),
        GenomicRanges (>= 1.54.1), ggplot2 (>= 3.4.4), ggpubr (>=
        0.6.0), ggtree (>= 3.8.0), graphics (>= 4.3.0), grDevices (>=
        4.3.0), igraph (>= 1.6.0), IRanges (>= 2.36.0), magrittr (>=
        2.0.3), OmicCircos (>= 1.44.0), pheatmap (>= 1.0.12), S4Vectors
        (>= 0.40.2), Seurat (== 4.3.0.1), Signac (>= 1.14.0), stats (>=
        4.3.0), TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.20.0), utils
        (>= 4.3.0)
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2025-09-25 03:55:18 UTC; 11565
