ChIPComp: Quantitative comparison of multiple ChIP-seq datasets

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

Author
Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang
Date of publication
None
Maintainer
Li Chen <li.chen@emory.edu>
License
GPL
Version
1.4.0

View on Bioconductor

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.

Files in this package

ChIPComp/DESCRIPTION
ChIPComp/NAMESPACE
ChIPComp/R
ChIPComp/R/ChIPComp.R
ChIPComp/R/makeCountSet.R
ChIPComp/R/utils.R
ChIPComp/build
ChIPComp/build/vignette.rds
ChIPComp/data
ChIPComp/data/seqData.rda
ChIPComp/inst
ChIPComp/inst/CITATION
ChIPComp/inst/NEWS
ChIPComp/inst/doc
ChIPComp/inst/doc/ChIPComp.R
ChIPComp/inst/doc/ChIPComp.Rnw
ChIPComp/inst/doc/ChIPComp.pdf
ChIPComp/inst/extdata
ChIPComp/inst/extdata/Helas3.ct.bed
ChIPComp/inst/extdata/Helas3.ip1.bed
ChIPComp/inst/extdata/Helas3.ip2.bed
ChIPComp/inst/extdata/Helas3.peak.bed
ChIPComp/inst/extdata/K562.ct.bed
ChIPComp/inst/extdata/K562.ip1.bed
ChIPComp/inst/extdata/K562.ip2.bed
ChIPComp/inst/extdata/K562.peak.bed
ChIPComp/inst/extdata/conf.csv
ChIPComp/inst/unitTests
ChIPComp/inst/unitTests/test_ChIPComp.R
ChIPComp/man
ChIPComp/man/ChIPComp-package.Rd
ChIPComp/man/ChIPComp.Rd
ChIPComp/man/makeConf.Rd
ChIPComp/man/makeCountSet.Rd
ChIPComp/man/plot.Rd
ChIPComp/man/print.Rd
ChIPComp/man/seqData.Rd
ChIPComp/src
ChIPComp/src/Makevars.win
ChIPComp/src/mva.c
ChIPComp/tests
ChIPComp/tests/runTests.R
ChIPComp/vignettes
ChIPComp/vignettes/ChIPComp.Rnw