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PSCBS  

Analysis of Parent-Specific DNA Copy Numbers
View on CRAN: Click here


Download and install PSCBS package within the R console
Install from CRAN:
install.packages("PSCBS")

Install from Github:
library("remotes")
install_github("cran/PSCBS")

Install by package version:
library("remotes")
install_version("PSCBS", "0.67.0")



Attach the package and use:
library("PSCBS")
Maintained by
Henrik Bengtsson
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2011-06-17
Latest Update: 2021-10-23
Description:
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.
How to cite:
Henrik Bengtsson (2011). PSCBS: Analysis of Parent-Specific DNA Copy Numbers. R package version 0.67.0, https://cran.r-project.org/web/packages/PSCBS. Accessed 22 Dec. 2024.
Previous versions and publish date:
0.11.0 (2011-06-17 20:22), 0.11.3 (2011-07-07 10:07), 0.11.7 (2011-07-23 15:03), 0.12.0 (2011-07-24 07:14), 0.12.1 (2011-08-08 07:41), 0.12.2 (2011-09-02 06:53), 0.15.4 (2011-11-02 18:16), 0.15.5 (2011-11-05 11:48), 0.16.0 (2011-11-14 07:41), 0.17.1 (2011-11-23 11:21), 0.19.4 (2012-01-11 08:02), 0.23.0 (2012-03-21 08:59), 0.28.1 (2012-08-19 07:30), 0.30.0 (2012-11-06 10:42), 0.34.8 (2013-04-21 08:11), 0.35.6 (2013-08-02 07:22), 0.37.0 (2013-09-21 22:57), 0.38.0 (2013-09-28 14:03), 0.38.4 (2013-10-16 11:35), 0.40.0 (2013-12-08 06:39), 0.40.4 (2014-02-05 17:31), 0.43.0 (2014-06-10 01:11), 0.44.0 (2015-02-23 00:20), 0.45.0 (2015-09-11 07:13), 0.45.1 (2015-09-17 07:51), 0.50.0 (2015-10-15 13:24), 0.60.0 (2015-11-18 09:31), 0.61.0 (2016-02-04 11:27), 0.62.0 (2016-11-11 00:23), 0.63.0 (2017-06-28 08:06), 0.64.0 (2018-08-12 22:50), 0.65.0 (2019-05-06 00:40), 0.66.0 (2021-10-23 09:40)
Other packages that cited PSCBS R package
View PSCBS citation profile
Other R packages that PSCBS depends, imports, suggests or enhances
Complete documentation for PSCBS
Functions, R codes and Examples using the PSCBS R package
Some associated functions: AbstractCBS . CBS . Non-documented_objects . NonPairedPSCBS . PSCBS-package . PSCBS . PairedPSCBS . Restructuring_AbstractCBS_objects . append.AbstractCBS . as.CBS.DNAcopy . as.DNAcopy.CBS . as.data.frame.AbstractCBS . as.data.frame.CBS . bootstrapTCNandDHByRegion.PairedPSCBS . c.CBS . callAB.PairedPSCBS . callAllelicBalanceByDH.PairedPSCBS . callAmplifications.CBS . callCopyNeutral.PairedPSCBS . callCopyNeutralByTCNofAB.PairedPSCBS . callGNL.PairedPSCBS . callGainsAndLosses.CBS . callLOH.PairedPSCBS . callOutliers.CBS . callROH.PairedPSCBS . callSegmentationOutliers . dropChangePoints.AbstractCBS . dropRegions.AbstractCBS . estimateDeltaAB.PairedPSCBS . estimateDeltaABBySmallDH.PairedPSCBS . estimateDeltaCN.PairedPSCBS . estimateDeltaLOH.PairedPSCBS . estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS . estimateKappa.PairedPSCBS . estimateKappaByC1Density.PairedPSCBS . estimateStandardDeviation.CBS . exampleData . extractMinorMajorCNs.PairedPSCBS . extractSegmentMeansByLocus.CBS . extractTCNAndDHs.PairedPSCBS . findLargeGaps . findNeutralCopyNumberState . gapsToSegments.data.frame . getBootstrapLocusSets.PairedPSCBS . getCallStatistics.CBS . getChromosomes.AbstractCBS . getFractionOfGenomeLost.CBS . getLocusData.AbstractCBS . getSampleName.AbstractCBS . getSegments.AbstractCBS . getSegments.PSCBS . getSmoothLocusData.CBS . hclustCNs.AbstractCBS . installDNAcopy . joinSegments.CBS . load.AbstractCBS . mergeNonCalledSegments.CBS . mergeThreeSegments.AbstractCBS . mergeTwoSegments.AbstractCBS . mergeTwoSegments.PairedPSCBS . nbrOfChangePoints.AbstractCBS . nbrOfChromosomes.AbstractCBS . nbrOfLoci.AbstractCBS . nbrOfSegments.AbstractCBS . normalizeTotalCNs.AbstractCBS . ploidy.AbstractCBS . plotTracks.AbstractCBS . plotTracks.CBS . plotTracks.PairedPSCBS . pruneByDP.AbstractCBS . pruneByHClust.AbstractCBS . pruneBySdUndo.CBS . randomSeed . report.AbstractCBS . resetSegments.AbstractCBS . save.AbstractCBS . segmentByCBS . segmentByNonPairedPSCBS . segmentByPairedPSCBS . setSampleName.AbstractCBS . testROH.numeric . updateMeans.AbstractCBS . updateMeansTogether.AbstractCBS . weightedQuantile . writeSegments.CBS . writeSegments.PSCBS . 
Some associated R codes: 000.R . 006.fixVarArgs.R . 999.DEPRECATED.R . 999.NonDocumentedObjects.R . 999.package.R . AbstractCBS.HCLUST.R . AbstractCBS.PLOT.R . AbstractCBS.PRUNE.R . AbstractCBS.R . AbstractCBS.REPORT.R . AbstractCBS.RESTRUCT.R . AbstractCBS.clearCalls.R . CBS.CALL.R . CBS.EXTS.R . CBS.IO.R . CBS.PLOT,many.R . CBS.PLOT.R . CBS.PRUNE.R . CBS.R . CBS.RESTRUCT.R . CBS.SMOOTH.R . CBS.joinSegments.R . CBS.updateMeansTogether.R . CNA.EXTS.R . DNAcopy.EXTS.R . NonPairedPSCBS.R . PSCBS.IO.R . PSCBS.R . PSCBS.RESTRUCT.R . PSCBS.isLocallyPhased.R . PairedPSCBS.BOOT.R . PairedPSCBS.BOOT.sets.R . PairedPSCBS.CALL.R . PairedPSCBS.EXTS.R . PairedPSCBS.EXTS3.R . PairedPSCBS.PLOT,many.R . PairedPSCBS.PLOT.R . PairedPSCBS.PLOT2.R . PairedPSCBS.PRUNE.R . PairedPSCBS.R . PairedPSCBS.RESTRUCT.R . PairedPSCBS.applyByRegion.R . PairedPSCBS.callAB.R . PairedPSCBS.callCopyNeutral.R . PairedPSCBS.callGNL.R . PairedPSCBS.callLOH.R . PairedPSCBS.callROH.R . PairedPSCBS.estimateDeltaAB.R . PairedPSCBS.estimateDeltaLOH.R . PairedPSCBS.estimateKappa.R . PairedPSCBS.extractSegmentDataByLocus.R . PairedPSCBS.unTumorBoost.R . PairedPSCBS.updateMeans.R . PairedPSCBS.updateMeansTogether.R . callSegmentationOutliers.R . drawLevels.DNAcopy.R . exampleData.R . findLargeGaps.R . findNeutralCopyNumberState.R . gapsToSegments.R . installDNAcopy.R . prememoize.R . randomSeed.R . segmentByCBS.R . segmentByNonPairedPSCBS.R . segmentByPairedPSCBS.R . testROH.R . utils.R . weightedQuantile.R . writeWIG.R . zzz.R .  Full PSCBS package functions and examples
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