consensusSeekeR

This is the development version of consensusSeekeR; for the stable release version, see consensusSeekeR.

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

Bioconductor version: Development (3.21)

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. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.

Author: Astrid Deschênes [cre, aut] (ORCID: ), Fabien Claude Lamaze [ctb], Pascal Belleau [aut] (ORCID: ), Arnaud Droit [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, ChIPSeq, Coverage, Genetics, MultipleComparison, PeakDetection, Sequencing, Software, Transcription
Version	1.35.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0), BiocGenerics, IRanges, GenomicRanges, BiocParallel
Imports	GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods
System Requirements
URL	https://github.com/adeschen/consensusSeekeR
Bug Reports	https://github.com/adeschen/consensusSeekeR/issues

Suggests	BiocStyle, ggplot2, knitr, rmarkdown, RUnit
Linking To
Enhances
Depends On Me
Imports Me	RJMCMCNucleosomes
Suggests Me	EpiCompare
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	consensusSeekeR_1.35.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/consensusSeekeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/consensusSeekeR
Bioc Package Browser	https://code.bioconductor.org/browse/consensusSeekeR/
Package Short Url	https://bioconductor.org/packages/consensusSeekeR/
Package Downloads Report	Download Stats