Package: SCOPE
Type: Package
Title: A normalization and copy number estimation method for
        single-cell DNA sequencing
Version: 1.25.0
Author: Rujin Wang, Danyu Lin, Yuchao Jiang
Maintainer: Rujin Wang <rujin@email.unc.edu>
Description: Whole genome single-cell DNA sequencing (scDNA-seq)
        enables characterization of copy number profiles at the
        cellular level. This circumvents the averaging effects
        associated with bulk-tissue sequencing and has increased
        resolution yet decreased ambiguity in deconvolving cancer
        subclones and elucidating cancer evolutionary history.
        ScDNA-seq data is, however, sparse, noisy, and highly variable
        even within a homogeneous cell population, due to the biases
        and artifacts that are introduced during the library
        preparation and sequencing procedure. Here, we propose SCOPE, a
        normalization and copy number estimation method for scDNA-seq
        data. The distinguishing features of SCOPE include: (i)
        utilization of cell-specific Gini coefficients for quality
        controls and for identification of normal/diploid cells, which
        are further used as negative control samples in a Poisson
        latent factor model for normalization; (ii) modeling of GC
        content bias using an expectation-maximization algorithm
        embedded in the Poisson generalized linear models, which
        accounts for the different copy number states along the genome;
        (iii) a cross-sample iterative segmentation procedure to
        identify breakpoints that are shared across cells from the same
        genetic background.
Depends: R (>= 3.6.0), GenomicRanges, IRanges, Rsamtools, GenomeInfoDb,
        BSgenome.Hsapiens.UCSC.hg19
Imports: stats, grDevices, graphics, utils, DescTools, RColorBrewer,
        gplots, foreach, parallel, doParallel, DNAcopy, BSgenome,
        Biostrings, BiocGenerics, S4Vectors
Suggests: knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
VignetteBuilder: knitr
biocViews: SingleCell, Normalization, CopyNumberVariation, Sequencing,
        WholeGenome, Coverage, Alignment, QualityControl, DataImport,
        DNASeq
License: GPL-2
LazyData: true
RoxygenNote: 6.1.1
Encoding: UTF-8
Config/pak/sysreqs: cmake make libbz2-dev liblzma-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:51:50 UTC
RemoteUrl: https://github.com/bioc/SCOPE
RemoteRef: HEAD
RemoteSha: 3cc19e682b10d081a198be19645cca91a77adecb
NeedsCompilation: no
Packaged: 2026-07-04 22:36:00 UTC; root