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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SCOPE" in publications use:'
type: software
license: GPL-2.0-only
title: 'SCOPE: A normalization and copy number estimation method for single-cell DNA
  sequencing'
version: 1.17.0
abstract: '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.'
authors:
- family-names: Wang
  given-names: Rujin
  email: rujin@email.unc.edu
- family-names: Lin
  given-names: Danyu
- family-names: Jiang
  given-names: Yuchao
repository: https://bioc.r-universe.dev
contact:
- family-names: Wang
  given-names: Rujin
  email: rujin@email.unc.edu