DNaseR: DNase I footprinting analysis of DNase-seq data

Strand-specific digital genomic footprinting in DNase-seq data. The cumulative Skellam distribution function (package 'skellam') is used to detect significant normalized count differences of opposed sign at each DNA strand. This is done in order to determine the protein-binding footprint flanks. Preprocessing of the mapped reads is recommended before running DNaseR (e.g., quality checking and removal of sequence-specific bias).

Author
Pedro Madrigal <pm12@sanger.ac.uk>
Date of publication
None
Maintainer
Pedro Madrigal <pm12@sanger.ac.uk>
License
GPL-2 + file LICENSE
Version
1.2.0

View on Bioconductor

Man pages

DNaseR-internal
DNaseR internal functions
DNaseR-package
DNase I footprinting analysis of DNase-seq data
footprints
DNase I footprinting analysis of DNase-seq data

Files in this package

DNaseR/DESCRIPTION
DNaseR/LICENSE
DNaseR/NAMESPACE
DNaseR/R
DNaseR/R/footprints.R
DNaseR/R/pskellam.R
DNaseR/R/pskellam.sp.R
DNaseR/build
DNaseR/build/vignette.rds
DNaseR/inst
DNaseR/inst/doc
DNaseR/inst/doc/DNaseR.R
DNaseR/inst/doc/DNaseR.Rnw
DNaseR/inst/doc/DNaseR.pdf
DNaseR/inst/extdata
DNaseR/inst/extdata/chrY_3Kb_wgEncodeUwDgfTh1Aln.bam
DNaseR/inst/extdata/chrY_3Kb_wgEncodeUwDgfTh1Aln.bam.bai
DNaseR/inst/unitTests
DNaseR/inst/unitTests/test_footprints.R
DNaseR/man
DNaseR/man/DNaseR-internal.Rd
DNaseR/man/DNaseR-package.Rd
DNaseR/man/footprints.Rd
DNaseR/tests
DNaseR/tests/runTests.R
DNaseR/vignettes
DNaseR/vignettes/DNaseR.Rnw