PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Version: 0.67.0
Depends: R (≥ 3.2.0)
Imports: R.methodsS3 (≥ 1.8.2), R.oo (≥ 1.25.0), R.utils (≥ 2.12.0), R.cache (≥ 0.16.0), matrixStats (≥ 0.62.0), aroma.light (≥ 2.4.0), DNAcopy (≥ 1.42.0), listenv (≥ 0.8.0), future (≥ 1.28.0), parallel, graphics, grDevices, stats, utils
Suggests: R.rsp (≥ 0.45.0), R.devices (≥ 2.17.1), ggplot2 (≥ 3.2.1)
Published: 2024-02-17
DOI: NA
Author: Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut], Venkatraman E. Seshan [aut], Adam B. Olshen [aut], Paul T. Spellman [aut], Richard A. Olshen [aut], Frank E Harrell Jr [ctb] (Weighted quantile estimator adopted from Hmisc::wtd.quantile())
Maintainer: Henrik Bengtsson <henrikb at braju.com>
BugReports: https://github.com/HenrikBengtsson/PSCBS/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/HenrikBengtsson/PSCBS
NeedsCompilation: no
Citation: PSCBS citation info
Materials: README NEWS
In views: Omics
CRAN checks: PSCBS results

Documentation:

Reference manual: PSCBS.pdf
Vignettes: Total copy-number segmentation using CBS
Parent-specific copy-number segmentation using Paired PSCBS

Downloads:

Package source: PSCBS_0.67.0.tar.gz
Windows binaries: r-devel: PSCBS_0.67.0.zip, r-release: PSCBS_0.67.0.zip, r-oldrel: PSCBS_0.67.0.zip
macOS binaries: r-release (arm64): PSCBS_0.67.0.tgz, r-oldrel (arm64): PSCBS_0.67.0.tgz, r-release (x86_64): PSCBS_0.67.0.tgz, r-oldrel (x86_64): PSCBS_0.67.0.tgz
Old sources: PSCBS archive

Reverse dependencies:

Reverse imports: aroma.cn, aroma.core, cfdnakit, EstMix
Reverse suggests: jointseg, PureCN

Linking:

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