GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GreyListChIP")
AuthorGord Brown <gdbzork@gmail.com>
Bioconductor views Alignment ChIPSeq Coverage DifferentialPeakCalling GenomeAnnotation Preprocessing Sequencing
Date of publicationNone
MaintainerGordon Brown <gordon.brown@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/greylist.R
build
build/vignette.rds
data
data/datalist
data/greyList.RData
inst
inst/NEWS.Rd
inst/doc
inst/doc/GreyList-demo.R
inst/doc/GreyList-demo.Rnw
inst/doc/GreyList-demo.pdf
inst/extra
inst/extra/karyotype_chr21.txt
inst/unitTests
inst/unitTests/test_loadKaryotype.R
man
man/GreyList-class.Rd man/calcThreshold-methods.Rd man/countReads-methods.Rd man/getKaryotype-methods.Rd man/greyList.Rd man/greyListBS.Rd man/loadKaryotype-methods.Rd man/makeGreyList-methods.Rd
tests
tests/runTests.R
vignettes
vignettes/GreyList-demo.Rnw
vignettes/GreyList.bib

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