BasicSTARRseq: Basic peak calling on STARR-seq data
Version 1.4.0

Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.

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AuthorAnnika Buerger
Bioconductor views Coverage FunctionalGenomics FunctionalPrediction GeneRegulation PeakDetection
Date of publicationNone
MaintainerAnnika Buerger <annika.buerger@ukmuenster.de>
LicenseLGPL-3
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BasicSTARRseq")

Man pages

getPeaks: Peak calling on STARR-seq data
STARRseqData-class: Class '"STARRseqData"'

Functions

STARRseqData Man page
STARRseqData,GRanges,GRanges,ANY-method Man page
STARRseqData,GRanges,GRanges-method Man page
STARRseqData,character,character,logical-method Man page
STARRseqData-class Man page
control Man page
control,STARRseqData-method Man page
control<- Man page
control<-,STARRseqData,GRanges-method Man page
correctConfInt Source code
getPeakPos Source code
getPeaks Man page
getPeaks,STARRseqData-method Man page
sample Man page
sample,STARRseqData-method Man page
sample<- Man page
sample<-,STARRseqData,GRanges-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.r
R/AllGenerics.r
R/getPeaks.R
R/methods-STARRseqData.r
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/BasicSTARRseq.R
inst/doc/BasicSTARRseq.pdf
inst/doc/BasicSTARRseq.rnw
inst/extdata
inst/extdata/smallInput.bam
inst/extdata/smallSTARR.bam
man
man/STARRseqData-class.Rd
man/getPeaks.Rd
vignettes
vignettes/BasicSTARRseq.rnw
BasicSTARRseq documentation built on May 20, 2017, 10:29 p.m.