SCOPE

DOI:10.18129/B9.bioc.SCOPE

This is thedevelopmentversion of SCOPE; for the stable release version, seeSCOPE.

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

Bioconductor version: Development (3.17)

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

Installation

To install this package, start R (version "4.3") 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 appropriateBioconductor release.

Documentation

查看文档的版本包age 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	1.11.0
In Bioconductor since	BioC 3.11 (R-4.0) (2.5 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
LinkingTo
Suggests	knitr,rmarkdown,WGSmapp,BSgenome.Hsapiens.UCSC.hg38,BSgenome.Mmusculus.UCSC.mm10,testthat(>= 2.1.0)
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Build Report

Package Archives

Followbob 体育网址 instructions to use this package in your R session.

Source Package	SCOPE_1.11.0.tar.gz
Windows Binary	SCOPE_1.11.0.zip
macOS Binary (x86_64)	SCOPE_1.11.0.tgz
macOS Binary (arm64)	SCOPE_1.11.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCOPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SCOPE
Bioc Package Browser	https://code.bioconductor.org/browse/SCOPE/
Package Short Url	//www.anjoumacpherson.com/packages/SCOPE/
Package Downloads Report	Download Stats