Package: PeakSegOptimal 2024.10.1

PeakSegOptimal: Optimal Segmentation Subject to Up-Down Constraints

Computes optimal changepoint models using the Poisson likelihood for non-negative count data, subject to the PeakSeg constraint: the first change must be up, second change down, third change up, etc. For more info about the models and algorithms, read "Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection" <https://jmlr.org/papers/v21/18-843.html> by TD Hocking et al.

Authors:Toby Dylan Hocking [aut, cre]

PeakSegOptimal_2024.10.1.tar.gz
PeakSegOptimal_2024.10.1.zip(r-4.7-x86_64)PeakSegOptimal_2024.10.1.zip(r-4.6-x86_64)PeakSegOptimal_2024.10.1.zip(r-4.5-x86_64)
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PeakSegOptimal_2024.10.1.tar.gz(r-4.7-arm64)PeakSegOptimal_2024.10.1.tar.gz(r-4.7-x86_64)PeakSegOptimal_2024.10.1.tar.gz(r-4.6-arm64)PeakSegOptimal_2024.10.1.tar.gz(r-4.6-x86_64)
PeakSegOptimal_2024.10.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html
DESCRIPTION |NEWS
card.svg |card.png
PeakSegOptimal/json (API)

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

Bug tracker:https://github.com/tdhock/peaksegoptimal/issues

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

On CRAN:

Conda:

cpp

3.69 score 6 stars 41 scripts 221 downloads 7 exports 19 dependencies

Last updated from:40b762a4ac. Checks:3 NOTE, 10 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64NOTE151
linux-devel-x86_64NOTE175
source / vignettesOK201
linux-release-arm64OK145
linux-release-x86_64OK170
macos-release-arm64OK174
macos-release-x86_64OK267
macos-oldrel-arm64OK137
macos-oldrel-x86_64OK259
windows-devel-x86_64NOTE224
windows-release-x86_64OK223
windows-oldrel-x86_64OK298
wasm-releaseOK107

Exports:oracleModelComplexityPeakSegFPOPPeakSegFPOPchromPeakSegPDPAPeakSegPDPAchromPeakSegPDPAInfPoissonLoss

Dependencies:clicpp11data.tablefarverggplot2gluegtableisobandlabelinglifecyclepenaltyLearningR6RColorBrewerrlangS7scalesvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
H3K4me3_PGP_immune ChIP-seq data set chunk 24H3K4me3_PGP_immune_chunk24
H3K4me3_XJ_immune chunk 1H3K4me3_XJ_immune_chunk1
oracleModelComplexityoracleModelComplexity
PeakSegFPOPPeakSegFPOP
PeakSegFPOPchromPeakSegFPOPchrom
PeakSegPDPAPeakSegPDPA
PeakSegPDPAchromPeakSegPDPAchrom
PeakSegPDPAInfPeakSegPDPAInf
PoissonLossPoissonLoss