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nucleoSim

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

Generate synthetic nucleosome maps


Bioconductor version: Development (3.19)

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 "4.4") 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 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License Artistic-2.0
Depends
Imports stats, IRanges, S4Vectors, graphics, methods
System Requirements
URL https://github.com/arnauddroitlab/nucleoSim
Bug Reports https://github.com/arnauddroitlab/nucleoSim/issues
See More
Suggests BiocStyle, BiocGenerics, knitr, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me RJMCMCNucleosomes
Links To Me
Build Report Build Report

Package Archives

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

Source Package nucleoSim_1.31.0.tar.gz
Windows Binary nucleoSim_1.31.0.zip
macOS Binary (x86_64) nucleoSim_1.31.0.tgz
macOS Binary (arm64) nucleoSim_1.31.0.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