nucleoSim

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Generate synthetic nucleosome maps

Bioconductor version: Development (3.24)

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] ORCID: 0000-0001-7846-6749 , Pascal Belleau [aut] ORCID: 0000-0002-0802-1071 , Arnaud Droit [aut]

Maintainer: Astrid Deschênes <adeschen at hotmail.com>

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

Rawane Samb, Astrid Deschênes, Pascal Belleau, Arnaud Droit. nucleoSim: Generate synthetic nucleosome maps. doi:10.18129/B9.bioc.nucleoSim, R package version 1.41.0, https://bioconductor.org/packages/nucleoSim.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Genetics, Sequencing, Software, StatisticalMethod
Version	1.41.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 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, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	RJMCMCNucleosomes
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	nucleoSim_1.41.0.tar.gz
Windows Binary (x86_64)	nucleoSim_1.41.0.zip
macOS Binary (big-sur-x86_64)	nucleoSim_1.41.0.tgz
macOS Binary (sonoma-arm64)	nucleoSim_1.41.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/nucleoSim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/nucleoSim
Package Short Url	https://bioconductor.org/packages/nucleoSim/
Package Downloads Report	Download Stats