consensusSeekeR

This package is for version 3.14 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: 3.14

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>

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

Installation

To install this package, start R (version "4.1") and enter:


if (!require("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")

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 1.22.0

In Bioconductor since BioC 3.3 (R-3.3) (8 years)

License Artistic-2.0

Depends R (>= 2.10), BiocGenerics, IRanges, GenomicRanges, BiocParallel

Imports GenomeInfoDb, rtracklayer, stringr, S4Vectors, methods

System Requirements

URL https://github.com/ArnaudDroitLab/consensusSeekeR

Bug Reports https://github.com/ArnaudDroitLab/consensusSeekeR/issues

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_1.22.0.tar.gz

Windows Binary consensusSeekeR_1.22.0.zip

macOS 10.13 (High Sierra) consensusSeekeR_1.22.0.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

Old Source Packages for BioC 3.14 Source Archive