BasicSTARRseq

DOI: 10.18129/B9.bioc.BasicSTARRseq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BasicSTARRseq.

Basic peak calling on STARR-seq data

Bioconductor version: 3.9

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.

Author: Annika Buerger

Maintainer: Annika Buerger <annika.buerger at ukmuenster.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BasicSTARRseq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BasicSTARRseq")

 

PDF	R Script	BasicSTARRseq.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Coverage, FunctionalGenomics, FunctionalPrediction, GeneRegulation, PeakDetection, Software
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	LGPL-3
Depends	GenomicRanges, GenomicAlignments
Imports	S4Vectors, methods, IRanges, GenomeInfoDb, stats
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BasicSTARRseq_1.12.0.tar.gz
Windows Binary	BasicSTARRseq_1.12.0.zip
Mac OS X 10.11 (El Capitan)	BasicSTARRseq_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BasicSTARRseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BasicSTARRseq
Package Short Url	https://bioconductor.org/packages/BasicSTARRseq/
Package Downloads Report	Download Stats