Package: copynumber 1.29.0.9000

Gro Nilsen

copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.

Authors:Gro Nilsen, Knut Liestoel and Ole Christian Lingjaerde.

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Bug tracker:https://github.com/igordot/copynumber/issues

On CRAN:

21 exports 14 stars 1.38 score 17 dependencies 75 scripts

Last updated 1 years agofrom:2e31d59f55. Checks:OK: 1 NOTE: 6. Indexed: yes.

Exports:aspcfcallAberrationsgetGRangesFormatimputeMissinginterpolate.pcfmultipcfpcfpcfPlainplotAberrationplotAlleleplotChromplotCircleplotFreqplotGammaplotGenomeplotHeatmapplotSampleselectSegmentssubsetDatasubsetSegmentswinsorize

Dependencies:askpassBiocGenericscurlGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6S4VectorssysUCSC.utilsXVectorzlibbioc