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SCOPE

This is the development version of SCOPE; for the stable release version, see SCOPE.

A normalization and copy number estimation method for single-cell DNA sequencing


Bioconductor version: Development (3.19)

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.

Author: Rujin Wang, Danyu Lin, Yuchao Jiang

Maintainer: Rujin Wang <rujin at email.unc.edu>

Citation (from within R, enter citation("SCOPE")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("SCOPE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Alignment, CopyNumberVariation, Coverage, DNASeq, DataImport, Normalization, QualityControl, Sequencing, SingleCell, Software, WholeGenome
Version 1.15.0
In Bioconductor since BioC 3.11 (R-4.0) (4 years)
License GPL-2
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
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Suggests knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
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Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
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macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SCOPE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SCOPE
Package Short Url https://bioconductor.org/packages/SCOPE/
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