Registration Open for Bioc2024
Early registration discount pricing ends May 31!

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 (3.20)

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 DeschĂȘnes [cre, aut] , Fabien Claude Lamaze [ctb], Pascal Belleau [aut] , Arnaud Droit [aut]

Maintainer: Astrid DeschĂȘnes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews BiologicalQuestion, ChIPSeq, Coverage, Genetics, MultipleComparison, PeakDetection, Sequencing, Software, Transcription
Version 1.33.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
See More
Suggests BiocStyle, ggplot2, knitr, rmarkdown, RUnit
Linking To
Enhances
Depends On Me
Imports Me RJMCMCNucleosomes
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package consensusSeekeR_1.33.0.tar.gz
Windows Binary consensusSeekeR_1.33.0.zip
macOS Binary (x86_64) consensusSeekeR_1.33.0.tgz
macOS Binary (arm64) consensusSeekeR_1.33.0.tgz
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