Package: PeakSegJoint 2024.10.1

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:Toby Dylan Hocking [aut, cre]

PeakSegJoint_2024.10.1.tar.gz
PeakSegJoint_2024.10.1.zip(r-4.5)PeakSegJoint_2024.10.1.zip(r-4.4)PeakSegJoint_2024.10.1.zip(r-4.3)
PeakSegJoint_2024.10.1.tgz(r-4.4-x86_64)PeakSegJoint_2024.10.1.tgz(r-4.4-arm64)PeakSegJoint_2024.10.1.tgz(r-4.3-x86_64)PeakSegJoint_2024.10.1.tgz(r-4.3-arm64)
PeakSegJoint_2024.10.1.tar.gz(r-4.5-noble)PeakSegJoint_2024.10.1.tar.gz(r-4.4-noble)
PeakSegJoint_2024.10.1.tgz(r-4.4-emscripten)PeakSegJoint_2024.10.1.tgz(r-4.3-emscripten)
PeakSegJoint.pdf |PeakSegJoint.html
PeakSegJoint/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

3.84 score 5 stars 46 scripts 773 downloads 15 exports 31 dependencies

Last updated 2 months agofrom:f8e7f9d12b. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-win-x86_64OKNov 01 2024
R-4.5-linux-x86_64OKNov 01 2024
R-4.4-win-x86_64OKNov 01 2024
R-4.4-mac-x86_64OKNov 01 2024
R-4.4-mac-aarch64OKNov 01 2024
R-4.3-win-x86_64OKNov 01 2024
R-4.3-mac-x86_64OKNov 01 2024
R-4.3-mac-aarch64OKNov 01 2024

Exports:binSumclusterPeaksConvertModelListfeatureMatrixJointmultiClusterPeaksPeakErrorSamplesPeakSegJointErrorPeakSegJointFasterPeakSegJointFasterOnePeakSegJointHeuristicPeakSegJointHeuristicStep1PeakSegJointHeuristicStep2PeakSegJointSeveralPoissonLossProfileList

Dependencies:clicolorspacedata.tablefansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmePeakErrorpenaltyLearningpillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
binSumbinSum
chr7 peakschr7.peaks
clusterPeaksclusterPeaks
ConvertModelListConvertModelList
Demo profilesdemo.profiles
featureMatrixJointfeatureMatrixJoint
GeomTallRectGeomTallRect
Some histone ChIP-seq dataH3K27ac.TDH.MMM4
H3K36me3_AM_immune chunk 21H3K36me3.AM.immune.chunk21
H3K36me3 TDH other chunk 1H3K36me3.TDH.other.chunk1
H3K4me3 PGP immune chunk 2H3K4me3.PGP.immune.chunk2
H3K4me3_TDH_other chunk 8 subsetH3K4me3.TDH.other.chunk8
multiClusterPeaksmultiClusterPeaks
Data set that caused integer overflowoverflow.list
peak at profile endpeak.at.profile.end
data where the PeakSegJoint model with 1 peak is infeasiblepeak1.infeasible
PeakErrorSamplesPeakErrorSamples
PeakSegJointErrorPeakSegJointError
PeakSegJointFasterPeakSegJointFaster
PeakSegJointFasterOnePeakSegJointFasterOne
PeakSegJointHeuristicPeakSegJointHeuristic
PeakSegJointHeuristicStep1PeakSegJointHeuristicStep1
PeakSegJointHeuristicStep2PeakSegJointHeuristicStep2
PeakSegJointSeveralPeakSegJointSeveral
PoissonLossPoissonLoss
ProfileListProfileList