DBChIP: Differential Binding of Transcription Factor with ChIP-seq
Version 1.20.0

DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.

Browse man pages Browse package API and functions Browse package files

AuthorKun Liang
Bioconductor views ChIPSeq Genetics Sequencing Transcription
Date of publicationNone
MaintainerKun Liang <kliang@stat.wisc.edu>
LicenseGPL (>= 2)
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DBChIP")

Man pages

binding.site.list: Binding site predictions
chip.data.list: ChIP data of transcription factor PHA-4/FOXA in _C.elegans_
conds: conds
DBChIP: DBChIP
DBChIP-package: DBChIP-package
get.site.count: Get site count
input.data.list: Control/input data of transcription factor PHA-4/FOXA in...
load.data: load.data
PHA4: ChIP-seq data of transcription factor PHA-4/FOXA in...
plotPeak: Plot peak
read.binding.site.list: read.binding.site.list
report.peak: Report peaks
site.merge: Cluster close-by sites into consensus sites
test.diff.binding: Test for differential binding

Functions

DBChIP Man page Source code
DBChIP-package Man page
MCS.list.merge Source code
MCS.merge Source code
NCIS Source code
NCIS.internal Source code
PHA4 Man page
bin.data Source code
binding.site.list Man page
chip.data.list Man page
combine.reps Source code
comp.background.size Source code
comp.bkg.size Source code
conds Man page
est.common.disp.by.collapse Source code
est.norm.med.search Source code
fdr Source code
get.NCIS.norm.factor Source code
get.binding.chr Source code
get.chr Source code
get.chr.len Source code
get.chr.site.count Source code
get.chr.unique.read.count Source code
get.cluster Source code
get.coverage Source code
get.site.count Man page Source code
get.site.count.hist Source code
get.unique.read.count Source code
get.unique.read.count.hist Source code
input.data.list Man page
load.data Man page Source code
median.ratio Source code
plotPeak Man page Source code
read.AlignedRead Source code
read.BED Source code
read.MCS Source code
read.MCS.list Source code
read.binding.site.list Man page Source code
read.data.list Source code
report.peak Man page Source code
single.peak Source code
site.merge Man page Source code
test.diff.binding Man page Source code
test.diff.binding.2sample Source code
test.diff.binding.DESeq Source code
test.diff.binding.edgeR Source code
unlist.data.frame Source code

Files

DESCRIPTION
NAMESPACE
R
R/DBChIP.R
R/NCIS.R
build
build/vignette.rds
data
data/PHA4.rda
data/datalist
inst
inst/doc
inst/doc/DBChIP.R
inst/doc/DBChIP.Rnw
inst/doc/DBChIP.pdf
inst/ext
inst/ext/L1.binding.txt
inst/ext/emb.binding.txt
inst/unitTests
inst/unitTests/runTests.R
inst/unitTests/test_all.R
man
man/DBChIP-package.Rd
man/DBChIP.Rd
man/PHA4.Rd
man/binding.site.list.Rd
man/chip.data.list.Rd
man/conds.Rd
man/get.site.count.Rd
man/input.data.list.Rd
man/load.data.Rd
man/plotPeak.Rd
man/read.binding.site.list.Rd
man/report.peak.Rd
man/site.merge.Rd
man/test.diff.binding.Rd
tests
tests/runTests.R
vignettes
vignettes/DBChIP.Rnw
vignettes/DBChIP.bib
DBChIP documentation built on May 20, 2017, 9:28 p.m.