SCOPE
A normalization and copy number estimation method for single-cell DNA sequencing
Bioconductor version: Release (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 <rujin at email.unc.edu>
citation("SCOPE")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| SCOPE: Single-cell Copy Number Estimation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, CopyNumberVariation, Coverage, DNASeq, DataImport, Normalization, QualityControl, Sequencing, SingleCell, Software, WholeGenome |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (3.5 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 |
| Linking To | |
| Suggests | knitr, rmarkdown, WGSmapp, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, testthat (>= 2.1.0) |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.12.0.tar.gz |
| Windows Binary | SCOPE_1.12.0.zip |
| macOS Binary (x86_64) | SCOPE_1.12.0.tgz |
| macOS Binary (arm64) | SCOPE_1.12.0.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 | https://bioconductor.org/packages/SCOPE/ |
| Package Downloads Report | Download Stats |