chipseq: chipseq: A package for analyzing chipseq data

Tools for helping process short read data for chipseq experiments

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chipseq")
AuthorDeepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao
Bioconductor views ChIPSeq Coverage DataImport QualityControl Sequencing
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version1.24.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/context.R R/diffPeaks.R R/filter.R R/fraglen.R R/intersect.R R/islands.R R/peaks.R R/plots.R R/subsets.R
TODO
build
build/vignette.rds
data
data/cstest.rda
data/datalist
inst
inst/Scripts
inst/Scripts/AntibodyComparison.Rnw
inst/Scripts/CTCFBindingSites.R inst/Scripts/CTCF_ERV.R
inst/Scripts/CopyNumber.Rnw
inst/Scripts/Islands.Rnw
inst/Scripts/MyoD.R
inst/Scripts/PairedEndComparison.Rnw
inst/Scripts/PeakContextHuman.Rnw
inst/Scripts/PeakContextMouse.Rnw
inst/Scripts/PeakCutoff.Rnw
inst/Scripts/PeakModel.Rnw
inst/Scripts/PeakReproducibility.Rnw
inst/Scripts/PeaksByCopyNumber.Rnw
inst/Scripts/RateComparison.Rnw
inst/Scripts/ReadAndSave54.R inst/Scripts/ReadAndSaveCTCF.R inst/Scripts/ReadAndSaveData.R inst/Scripts/ReadAndSaveSimulation.R inst/Scripts/SolexaSim.R
inst/Scripts/abc.rda
inst/Scripts/antibody_comparison.R inst/Scripts/dePeaks.R inst/Scripts/diffpeak.R inst/Scripts/diffpeaks.R inst/Scripts/estimate_fragment_size.R inst/Scripts/fibroblasts.R
inst/Scripts/figs
inst/Scripts/getIsochores.R inst/Scripts/hmm.R inst/Scripts/human-islands.R inst/Scripts/isochore_comparison.R
inst/Scripts/isochores.mm9.rda
inst/Scripts/negbinomial.R inst/Scripts/peakContext.R inst/Scripts/peak_mle.R inst/Scripts/poisson.R inst/Scripts/simulate.R
inst/Scripts/singletons.Rnw
inst/Scripts/solexa54.R
inst/doc
inst/doc/Workflow.R
inst/doc/Workflow.Rnw
inst/doc/Workflow.pdf
man
man/chipseqFilter.Rd man/coverageplot.Rd man/cstest.Rd man/diffPeakSummary.Rd man/estimate.mean.fraglen.Rd man/islandDepthPlot.Rd man/laneSubsample.Rd man/peakCutoff.Rd man/peakSummary-methods.Rd man/subsetSummary.Rd
src
src/rlesumprod.c
vignettes
vignettes/Workflow.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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