chipseq: chipseq: A package for analyzing chipseq data

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Tools for helping process short read data for chipseq experiments

Author
Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
1.24.0

View on Bioconductor

Man pages

chipseqFilter
Filtering ChIP-seq reads
coverageplot
Plot coverage on a small interval.
cstest
A test ChIP-Seq dataset
diffPeakSummary
A function to identify and produce summary statistics for...
estimate.mean.fraglen
Estimate summaries of the distribution of fragment lengths in...
islandDepthPlot
Plot island depth distribution
laneSubsample
Subsample short read alignment locations
peakCutoff
Calculate a peak cutoff
peakSummary-methods
Summarizing peak sets
subsetSummary
Compute summaries for cumulative subsets of a short-read data...

Files in this package

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