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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: 10.32614/CRAN.package.PSCBS
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:

Please use the canonical form https://CRAN.R-project.org/package=PSCBS 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.