DNaseR: DNase I footprinting analysis of DNase-seq data
Version 1.2.0

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).

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AuthorPedro Madrigal <pm12@sanger.ac.uk>
Date of publicationNone
MaintainerPedro Madrigal <pm12@sanger.ac.uk>
LicenseGPL-2 + file LICENSE
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DNaseR")

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

Functions

Files

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
DNaseR documentation built on Sept. 12, 2016, 6:05 a.m.