DBChIP: Differential Binding of Transcription Factor with ChIP-seq

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

Author
Kun Liang
Date of publication
None
Maintainer
Kun Liang <kliang@stat.wisc.edu>
License
GPL (>= 2)
Version
1.18.0

View on Bioconductor

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

Files in this package

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