scquantum: Estimate Ploidy and Absolute Copy Number from Single Cell Sequencing

Given bincount data from single-cell copy number profiling (segmented or unsegmented), estimates ploidy, and uses the ploidy estimate to scale the data to absolute copy numbers. Uses the modular quantogram proposed by Kendall (1986) <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting segments according to confidence, and quantifying confidence in the estimate using a theoretical quantogram. Includes optional fused-lasso segmentation with the algorithm in Johnson (2013) <doi:10.1080/10618600.2012.681238>, using the implementation from glmgen by Arnold, Sadhanala, and Tibshirani.

Version: 1.0.0
Suggests: testthat (≥ 3.0.0)
Published: 2022-03-23
DOI: 10.32614/CRAN.package.scquantum
Author: Alexander Davis [aut, cre], Taylor Arnold [cph] (Author of segmentation function), Veeranjaneyulu Sadhanala [cph] (Author of segmentation function), Ryan Tibshirani [cph] (Author of segmentation function)
Maintainer: Alexander Davis <alexlovesmolecules at>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Materials: README
CRAN checks: scquantum results


Reference manual: scquantum.pdf


Package source: scquantum_1.0.0.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): scquantum_1.0.0.tgz, r-oldrel (arm64): scquantum_1.0.0.tgz, r-release (x86_64): scquantum_1.0.0.tgz, r-oldrel (x86_64): scquantum_1.0.0.tgz


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