Package: SCOPE
Type: Package
Title: A normalization and copy number estimation method for
        single-cell DNA sequencing
Version: 1.22.0
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
git_url: https://git.bioconductor.org/packages/SCOPE
git_branch: RELEASE_3_22
git_last_commit: a28af97
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 04:09:02 UTC; biocbuild
Built: R 4.5.1; ; 2025-10-30 09:40:12 UTC; unix
