nucleoSim

DOI: 10.18129/B9.bioc.nucleoSim  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see nucleoSim.

Generate synthetic nucleosome maps

Bioconductor version: 3.16

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 "4.2") 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 1.26.0
In Bioconductor since BioC 3.3 (R-3.3) (7 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_1.26.0.tar.gz
Windows Binary nucleoSim_1.26.0.zip
macOS Binary (x86_64) nucleoSim_1.26.0.tgz
macOS Binary (arm64) nucleoSim_1.26.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: