nucleoSim

DOI: 10.18129/B9.bioc.nucleoSim  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see nucleoSim.

Generate synthetic nucleosome maps

Bioconductor version: 3.17

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

Author: Rawane Samb [aut], Astrid Deschênes [cre, aut] , Pascal Belleau [aut] , Arnaud Droit [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("nucleoSim")

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("nucleoSim")

 

HTML	R Script	Generate synthetic nucleosome maps
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Genetics, Sequencing, Software, StatisticalMethod
Version	1.28.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends
Imports	stats, IRanges, S4Vectors, graphics, methods
LinkingTo
Suggests	BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://github.com/arnauddroitlab/nucleoSim
BugReports	https://github.com/arnauddroitlab/nucleoSim/issues
Depends On Me
Imports Me
Suggests Me	RJMCMCNucleosomes
Links To Me
Build Report

Package Archives

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

Source Package	nucleoSim_1.28.0.tar.gz
Windows Binary	nucleoSim_1.28.0.zip
macOS Binary (x86_64)	nucleoSim_1.28.0.tgz
macOS Binary (arm64)	nucleoSim_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nucleoSim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nucleoSim
Bioc Package Browser	https://code.bioconductor.org/browse/nucleoSim/
Package Short Url	https://bioconductor.org/packages/nucleoSim/
Package Downloads Report	Download Stats