consensusSeekeR
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Bioconductor version: Release (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 Deschênes [cre, aut] 
, Fabien Claude Lamaze [ctb], Pascal Belleau [aut] , Arnaud Droit [aut]
Maintainer: Astrid Deschênes <adeschen at hotmail.com>
citation("consensusSeekeR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | BiologicalQuestion, ChIPSeq, Coverage, Genetics, MultipleComparison, PeakDetection, Sequencing, Software, Transcription |
| Version | 1.34.0 |
| 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 |
See More
| 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_1.34.0.tar.gz |
| Windows Binary (x86_64) | consensusSeekeR_1.34.0.zip |
| macOS Binary (x86_64) | consensusSeekeR_1.34.0.tgz |
| macOS Binary (arm64) | consensusSeekeR_1.34.0.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 |