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PeakSegJoint (version 2022.4.6)

Joint Peak Detection in Several ChIP-Seq Samples

Description

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" by TD Hocking and G Bourque.

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install.packages('PeakSegJoint')

Monthly Downloads

740

Version

2022.4.6

License

GPL-3

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Maintainer

Toby Hocking

Last Published

April 7th, 2022

Functions in PeakSegJoint (2022.4.6)

PeakSegJointError

PeakSegJointError
PeakSegJointFaster

PeakSegJointFaster
PeakSegJointHeuristic

PeakSegJointHeuristic
PeakSegJointFasterOne

PeakSegJointFasterOne
demo.profiles

Demo profiles
chr7.peaks

chr7 peaks
clusterPeaks

clusterPeaks
featureMatrixJoint

featureMatrixJoint
PoissonLoss

PoissonLoss
PeakSegJointSeveral

PeakSegJointSeveral
H3K4me3.PGP.immune.chunk2

H3K4me3 PGP immune chunk 2
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
ProfileList

ProfileList
peak.at.profile.end

peak at profile end
peak1.infeasible

data where the PeakSegJoint model with 1 peak is infeasible
binSum

binSum
multiClusterPeaks

multiClusterPeaks
PeakSegJointHeuristicStep2

PeakSegJointHeuristicStep2
overflow.list

Data set that caused integer overflow
PeakSegJointHeuristicStep1

PeakSegJointHeuristicStep1
GeomTallRect

GeomTallRect
ConvertModelList

ConvertModelList
PeakErrorSamples

PeakErrorSamples
H3K4me3.TDH.other.chunk8

H3K4me3_TDH_other chunk 8 subset