Bioconductor - consensusSeekeR

Bioconductor - consensusSeekeR
Bioconductor 3.22
Software Packages
consensusSeekeR
consensusSeekeR
This is the
released
version of consensusSeekeR; for the devel version, see
consensusSeekeR
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
DOI:
10.18129/B9.bioc.consensusSeekeR
Bioconductor version:
Release (3.22)
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: 0000-0001-7846-6749
, Fabien Claude Lamaze [ctb], Pascal Belleau [aut]
ORCID: 0000-0002-0802-1071
, Arnaud Droit [aut]
Maintainer:
Astrid Deschênes
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")

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
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Details
biocViews
BiologicalQuestion
ChIPSeq
Coverage
Genetics
MultipleComparison
PeakDetection
Sequencing
Software
Transcription
Version
1.38.0
In Bioconductor since
BioC 3.3 (R-3.3) (10 years)
License
Artistic-2.0
Depends
R (>= 3.5.0),
BiocGenerics
IRanges
GenomicRanges
BiocParallel
Imports
Seqinfo
rtracklayer
stringr
S4Vectors
, methods
System Requirements
URL
Bug Reports
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_1.38.0.tar.gz
Windows Binary (x86_64)
consensusSeekeR_1.38.0.zip
(64-bit only)
macOS Binary (x86_64)
consensusSeekeR_1.38.0.tgz
macOS Binary (arm64)
consensusSeekeR_1.38.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/consensusSeekeR
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/consensusSeekeR
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