Package: PeakSegJoint 2024.12.4
PeakSegJoint: Joint Peak Detection in Several ChIP-Seq Samples
Jointly segment several ChIP-seq samples to find the peaks which are the same and different across samples. The fast approximate maximum Poisson likelihood algorithm is described in "PeakSegJoint: fast supervised peak detection via joint segmentation of multiple count data samples" <doi:10.48550/arXiv.1506.01286> by TD Hocking and G Bourque.
Authors:
PeakSegJoint_2024.12.4.tar.gz
PeakSegJoint_2024.12.4.zip(r-4.7)PeakSegJoint_2024.12.4.zip(r-4.6)PeakSegJoint_2024.12.4.zip(r-4.5)
PeakSegJoint_2024.12.4.tgz(r-4.6-x86_64)PeakSegJoint_2024.12.4.tgz(r-4.6-arm64)PeakSegJoint_2024.12.4.tgz(r-4.5-x86_64)PeakSegJoint_2024.12.4.tgz(r-4.5-arm64)
PeakSegJoint_2024.12.4.tar.gz(r-4.7-arm64)PeakSegJoint_2024.12.4.tar.gz(r-4.7-x86_64)PeakSegJoint_2024.12.4.tar.gz(r-4.6-arm64)PeakSegJoint_2024.12.4.tar.gz(r-4.6-x86_64)
PeakSegJoint_2024.12.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PeakSegJoint/json (API)
| # Install 'PeakSegJoint' in R: |
| install.packages('PeakSegJoint', repos = c('https://tdhock.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tdhock/peaksegjoint/issues
- chr7.peaks - Chr7 peaks
- demo.profiles - Demo profiles
- H3K27ac.TDH.MMM4 - Some histone ChIP-seq data
- H3K36me3.AM.immune.chunk21 - H3K36me3_AM_immune chunk 21
- H3K36me3.TDH.other.chunk1 - H3K36me3 TDH other chunk 1
- H3K4me3.PGP.immune.chunk2 - H3K4me3 PGP immune chunk 2
- H3K4me3.TDH.other.chunk8 - H3K4me3_TDH_other chunk 8 subset
- overflow.list - Data set that caused integer overflow
- peak.at.profile.end - Peak at profile end
- peak1.infeasible - Data where the PeakSegJoint model with 1 peak is infeasible
Last updated from:4d094840d3. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 262 | ||
| linux-devel-x86_64 | OK | 266 | ||
| source / vignettes | OK | 186 | ||
| linux-release-arm64 | OK | 288 | ||
| linux-release-x86_64 | OK | 252 | ||
| macos-release-arm64 | OK | 183 | ||
| macos-release-x86_64 | OK | 456 | ||
| macos-oldrel-arm64 | OK | 208 | ||
| macos-oldrel-x86_64 | OK | 353 | ||
| windows-devel | OK | 255 | ||
| windows-release | OK | 264 | ||
| windows-oldrel | OK | 266 | ||
| wasm-release | OK | 97 |
Exports:binSumclusterPeaksConvertModelListfeatureMatrixJointmultiClusterPeaksPeakErrorSamplesPeakSegJointErrorPeakSegJointFasterPeakSegJointFasterOnePeakSegJointHeuristicPeakSegJointHeuristicStep1PeakSegJointHeuristicStep2PeakSegJointSeveralPoissonLossProfileList
Dependencies:clicpp11data.tablefarverggplot2gluegtableisobandlabelinglifecyclePeakErrorpenaltyLearningR6RColorBrewerrlangS7scalesvctrsviridisLitewithr
