ChIPComp: Quantitative comparison of multiple ChIP-seq datasets
Version 1.6.0

ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.

Browse man pages Browse package API and functions Browse package files

AuthorHao Wu, Li Chen, Zhaohui S.Qin, Chi Wang
Bioconductor views ChIPSeq Coverage DataImport Genetics MultipleComparison Sequencing Transcription
Date of publicationNone
MaintainerLi Chen <li.chen@emory.edu>
LicenseGPL
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPComp")

Man pages

ChIPComp: Perform hypothesis testing to detect differential binding...
ChIPComp-package: Detect differential binding sites for ChIP sequencing data
makeConf: make configurations for experimental design written in csv...
makeCountSet: make differential binding sites data frame
plot: plot correlation between log ChIP read counts and smoothing...
print: Print top ranked differential binding sites
seqData: A 'ChIPComp' object.

Functions

ChIPComp Man page Source code
ChIPComp-package Man page
MACS.mva Source code
findCommonPeak Source code
findReplicate Source code
getCTCounts Source code
getWinCounts Source code
makeCTSet Source code
makeConf Man page Source code
makeCountSet Man page Source code
makeIPSet Source code
makePeakSet Source code
plot.ChIPComp Man page Source code
print.ChIPComp Man page Source code
read.BAM Source code
regress Source code
rmdup Source code
seqData Man page

Files

DESCRIPTION
NAMESPACE
R
R/ChIPComp.R
R/makeCountSet.R
R/utils.R
build
build/vignette.rds
data
data/seqData.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ChIPComp.R
inst/doc/ChIPComp.Rnw
inst/doc/ChIPComp.pdf
inst/extdata
inst/extdata/Helas3.ct.bed
inst/extdata/Helas3.ip1.bed
inst/extdata/Helas3.ip2.bed
inst/extdata/Helas3.peak.bed
inst/extdata/K562.ct.bed
inst/extdata/K562.ip1.bed
inst/extdata/K562.ip2.bed
inst/extdata/K562.peak.bed
inst/extdata/conf.csv
inst/unitTests
inst/unitTests/test_ChIPComp.R
man
man/ChIPComp-package.Rd
man/ChIPComp.Rd
man/makeConf.Rd
man/makeCountSet.Rd
man/plot.Rd
man/print.Rd
man/seqData.Rd
src
src/Makevars.win
src/mva.c
tests
tests/runTests.R
vignettes
vignettes/ChIPComp.Rnw
ChIPComp documentation built on May 20, 2017, 10:07 p.m.