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seqCBS
View on CRAN: Click
here
Download and install seqCBS package within the R console
Install from CRAN:
install.packages("seqCBS")
Install from Github:
library("remotes")
install_github("cran/seqCBS")
Install by package version:
library("remotes")
install_version("seqCBS", "1.2.1")
Attach the package and use:
library("seqCBS")
Maintained by
Jeremy J. Shen
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2010-10-25
Latest Update: 2019-04-13
Description:
This is a method for DNA Copy Number Profiling using
Next-Generation Sequencing. It has new model and test
statistics based on non-homogeneous Poisson Processes with
change point models. It uses an adaptation of Circular Binary
Segmentation. Also included are methods for point-wise Bayesian
Confidence Interval and model selection method for the
change-point model. A case and a control sample reads (normal
and tumor) are required.
How to cite:
Jeremy J. Shen (2010). seqCBS: Copy Number Profiling using Sequencing and CBS. R package version 1.2.1, https://cran.r-project.org/web/packages/seqCBS. Accessed 07 Nov. 2024.
Previous versions and publish date:
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Other R packages that seqCBS depends,
imports, suggests or enhances
Functions, R codes and Examples using
the seqCBS R package
Some associated functions: BayesCptCI . CombineCaseControlC . CombineReadsAcrossRuns . JSSim_Meta . JSSim_NormalSim1 . JSSim_NormalSim2 . JSSim_SpikeMat . JSSim_TumorSim1 . JSSim_TumorSim2 . ScanBIC . ScanCBS . ScanCBSPlot . ScanCBSSimPlot . ScanIterateGrid . ScanStatNewComp . ScanStatRefineComp . SegSeqResProcess . getAutoGridSize . getCountsInWindow . hppSimulate . nhppRateEstimate . nhppSimConstWindowAnalysis . nhppSimConstWindowGen . nhppSimulate . nhppSpike . nhppSpikeConstWindow . readInput . readListInputFile . readSeq . readSeqChiang . readSeqELANDPaired . relCNComp . seqCBS-package .
Some associated R codes: BayesCptCI.R . CombineCaseControlC.R . CombineReadsAcrossRuns.R . ScanBIC.R . ScanCBS.R . ScanCBSPlot.R . ScanCBSSimPlot.R . ScanIterateGrid.R . ScanStatNewComp.R . ScanStatRefineComp.R . SegSeqResProcess.R . getAutoGridSize.R . getCountsInWindow.R . hppSimulate.R . nhppRateEstimate.R . nhppSimConstWindowAnalysis.R . nhppSimConstWindowGen.R . nhppSimulate.R . nhppSpike.R . nhppSpikeConstWindow.R . readInput.R . readListInputFile.R . readSeq.R . readSeqChiang.R . readSeqELANDPaired.R . relCNComp.R . Full seqCBS package functions and examples
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