chipseq: chipseq: A package for analyzing chipseq data
Version 1.26.0

Tools for helping process short read data for chipseq experiments

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
Version1.26.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chipseq")

Popular man pages

chipseqFilter: Filtering ChIP-seq reads
coverageplot: Plot coverage on a small interval.
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
subsetSummary: Compute summaries for cumulative subsets of a short-read data...
See all...

All man pages Function index File listing

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...

Functions

RleSumAny Source code
RleSumProd Source code
applyPosByChrAndStrand Source code
basesCovered Man page Source code
chipseqFilter Man page Source code
correlation.estimate Source code
correlationProfile Source code
coverage.estimate Source code
coverageplot Man page Source code
cstest Man page
dKernel Source code
densityCorr Man page
densityCorr,GenomicRanges Man page
densityCorr,list Man page
diffPeakSummary Man page
diffPeakSummary,RleViewsList,RleViewsList-method Man page
doDensity1 Source code
doDensity2 Source code
doDensity3 Source code
estimate.bg.rate Source code
estimate.mean.fraglen Man page Source code
estimate.mean.fraglen,AlignedRead-method Man page
estimate.mean.fraglen,GRanges-method Man page
genomicContext Source code
islandDepthPlot Man page Source code
jothi.estimate Source code
laneSubsample Man page Source code
nearestTss Source code
peakCutoff Man page Source code
peakSummary Man page
peakSummary,RleViews-method Man page
peakSummary,RleViewsList-method Man page
peakSummary-methods Man page
removeIsolated Source code
rle_sum_prod_prototype Source code
similarity.corr Source code
sparse.density Man page Source code
subsetSummary Man page Source code

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
chipseq documentation built on May 20, 2017, 9:52 p.m.

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