SCOPE

DOI: 10.18129/B9.bioc.SCOPE    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SCOPE.

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

Bioconductor version: 3.12

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>

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("SCOPE")

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SCOPE")

 

HTML	R Script	SCOPE: Single-cell Copy Number Estimation
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, CopyNumberVariation, Coverage, DNASeq, DataImport, Normalization, QualityControl, Sequencing, SingleCell, Software, WholeGenome
Version	1.2.0
In Bioconductor since	BioC 3.11 (R-4.0) (1 year)
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
LinkingTo
Suggests	knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SCOPE_1.2.0.tar.gz
Windows Binary	SCOPE_1.2.0.zip
macOS 10.13 (High Sierra)	SCOPE_1.2.0.tgz
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/
Package Downloads Report	Download Stats