Package: jointseg 1.0.2

jointseg: Joint Segmentation of Multivariate (Copy Number) Signals

Methods for fast segmentation of multivariate signals into piecewise constant profiles and for generating realistic copy-number profiles. A typical application is the joint segmentation of total DNA copy numbers and allelic ratios obtained from Single Nucleotide Polymorphism (SNP) microarrays in cancer studies. The methods are described in Pierre-Jean, Rigaill and Neuvial (2015) <doi:10.1093/bib/bbu026>.

Authors:Morgane Pierre-Jean [aut, cre], Pierre Neuvial [aut], Guillem Rigaill [aut]

jointseg_1.0.2.tar.gz
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jointseg_1.0.2.tgz(r-4.6-x86_64)jointseg_1.0.2.tgz(r-4.6-arm64)jointseg_1.0.2.tgz(r-4.5-x86_64)jointseg_1.0.2.tgz(r-4.5-arm64)
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jointseg_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
jointseg/json (API)

# Install 'jointseg' in R:
install.packages('jointseg', repos = c('https://mpierrejean.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mpierrejean/jointseg/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

cpp

6.71 score 7 stars 2 packages 61 scripts 357 downloads 25 exports 3 dependencies

Last updated from:5b7ab68d33. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK150
linux-devel-x86_64OK137
source / vignettesOK183
linux-release-arm64OK151
linux-release-x86_64OK144
macos-release-arm64OK138
macos-release-x86_64OK302
macos-oldrel-arm64OK185
macos-oldrel-x86_64OK245
windows-develOK106
windows-releaseOK209
windows-oldrelOK96
wasm-releaseOK119

Exports:anotherBkpbinMissingValuesdefaultWeightsdoCBSdoDynamicProgrammingdoGFLarsdoPSCBSdoPSCNdoRBSestimateSdFpsngetCopyNumberDataByResamplinggetTpFpjointSegleftMultiplyByInvXAtXAleftMultiplyByXtmodelSelectionmultiplyXtXBySparseoneBkpplotSegpruneByDPPSSegrandomProfilesegmentByGFLarssegmentByRBS

Dependencies:acnrDNAcopymatrixStats

Generating realistic data with known truth using the jointseg package
Citing jointseg | Setup | Affymetrix data | Illumina data | Session information | References
Rendered fromdataGeneration.Rmdusingknitr::rmarkdown

Last update: 2019-01-07
Started: 2016-12-16

PSSeg: Parent-Specifc copy number segmentation
Preparing data to be segmented | Preprocessing | PSSeg segmentation using RBS | Initial segmentation and pruning | Plot segmented profile | Results evaluation | Session information | Citing jointseg | References
Rendered fromPSSeg.Rmdusingknitr::rmarkdown

Last update: 2017-11-30
Started: 2016-12-15