The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

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 gmail.com>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Materials: README
CRAN checks: scquantum results

Documentation:

Reference manual: scquantum.pdf

Downloads:

Package source: scquantum_1.0.0.tar.gz
Windows binaries: r-devel: scquantum_1.0.0.zip, r-release: scquantum_1.0.0.zip, r-oldrel: scquantum_1.0.0.zip
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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=scquantum to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.