Package: PeakSegJoint 2024.12.4
Toby Dylan Hocking
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.tar.gz(r-4.5-noble)PeakSegJoint_2024.12.4.tar.gz(r-4.4-noble)
PeakSegJoint_2024.12.4.tgz(r-4.4-emscripten)PeakSegJoint_2024.12.4.tgz(r-4.3-emscripten)
PeakSegJoint.pdf |PeakSegJoint.html✨
PeakSegJoint/json (API)
NEWS
| # Install 'PeakSegJoint' in R: |
| install.packages('PeakSegJoint', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tdhock/peaksegjoint/issues
- 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
- chr7.peaks - Chr7 peaks
- demo.profiles - Demo profiles
- 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 20 days agofrom:11cd511ece. Checks:OK: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 04 2024 |
| R-4.5-linux-x86_64 | OK | Dec 04 2024 |
Exports:binSumclusterPeaksConvertModelListfeatureMatrixJointmultiClusterPeaksPeakErrorSamplesPeakSegJointErrorPeakSegJointFasterPeakSegJointFasterOnePeakSegJointHeuristicPeakSegJointHeuristicStep1PeakSegJointHeuristicStep2PeakSegJointSeveralPoissonLossProfileList
Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmePeakErrorpenaltyLearningpillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
