nucleoSim

This is the development version of nucleoSim; for the stable release version, see nucleoSim.

Generate synthetic nucleosome maps

Bioconductor version: Development (3.18)

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>

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

Installation

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

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Details

biocViews	Alignment, Genetics, Sequencing, Software, StatisticalMethod
Version	1.29.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends
Imports	stats, IRanges, S4Vectors, graphics, methods
Linking To
Suggests	BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
System Requirements
Enhances
URL	https://github.com/arnauddroitlab/nucleoSim
Bug Reports	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_1.29.0.tar.gz
Windows Binary	nucleoSim_1.29.0.zip
macOS Binary (x86_64)	nucleoSim_1.29.0.tgz
macOS Binary (arm64)	nucleoSim_1.29.0.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