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BasicSTARRseq

Basic peak calling on STARR-seq data


Bioconductor version: Release (3.18)

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>

Citation (from within R, enter citation("BasicSTARRseq")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
BasicSTARRseq.pdf PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, FunctionalGenomics, FunctionalPrediction, GeneRegulation, PeakDetection, Software
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License LGPL-3
Depends GenomicRanges, GenomicAlignments
Imports S4Vectors, methods, IRanges, GenomeInfoDb, stats
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Suggests knitr
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Package Archives

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

Source Package BasicSTARRseq_1.30.0.tar.gz
Windows Binary BasicSTARRseq_1.30.0.zip
macOS Binary (x86_64) BasicSTARRseq_1.30.0.tgz
macOS Binary (arm64) BasicSTARRseq_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BasicSTARRseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BasicSTARRseq
Bioc Package Browser https://code.bioconductor.org/browse/BasicSTARRseq/
Package Short Url https://bioconductor.org/packages/BasicSTARRseq/
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