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.

AuthorGord Brown <gdbzork@gmail.com>
Date of publicationNone
MaintainerGordon Brown <gordon.brown@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version1.6.0

View on Bioconductor

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.