nucleoSim

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see nucleoSim.

Generate synthetic nucleosome maps

Bioconductor version: 3.10

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 user has choice between three different distributions for the read positioning: Normal, Student and Uniform.

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

Maintainer: Astrid Deschenes <adeschen at hotmail.com>

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

Installation

To install this package, start R (version "3.6") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Genetics, Sequencing, Software, StatisticalMethod
Version	1.14.0
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

Suggests	BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit
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_1.14.0.tar.gz
Windows Binary	nucleoSim_1.14.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	nucleoSim_1.14.0.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
Old Source Packages for BioC 3.10	Source Archive