consensusSeekeR

DOI: 10.18129/B9.bioc.consensusSeekeR    

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

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Bioconductor version: 3.9

This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.

Author: Astrid Deschenes [cre, aut], Fabien Claude Lamaze [ctb], Pascal Belleau [aut], Arnaud Droit [aut]

Maintainer: Astrid Deschenes <adeschen at hotmail.com>

Installation

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

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

BiocManager::install("consensusSeekeR")

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("consensusSeekeR")

 

HTML	R Script	Detection of consensus regions inside a group of experiments
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, ChIPSeq, Coverage, Genetics, MultipleComparison, PeakDetection, Sequencing, Software, Transcription
Version	1.12.0
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	Artistic-2.0
Depends	R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel
Imports	GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
LinkingTo
Suggests	BiocStyle, ggplot2, knitr, rmarkdown, RUnit
SystemRequirements
Enhances
URL	https://github.com/ArnaudDroitLab/consensusSeekeR
BugReports	https://github.com/ArnaudDroitLab/consensusSeekeR/issues
Depends On Me
Imports Me	RJMCMCNucleosomes
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	consensusSeekeR_1.12.0.tar.gz
Windows Binary	consensusSeekeR_1.12.0.zip
Mac OS X 10.11 (El Capitan)	consensusSeekeR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/consensusSeekeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/consensusSeekeR
Package Short Url	https://bioconductor.org/packages/consensusSeekeR/
Package Downloads Report	Download Stats