nucleoSim
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see nucleoSim.
Generate synthetic nucleosome maps
Bioconductor version: 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("nucleoSim")):
Installation
To install this package, start R (version "4.3") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Genetics, Sequencing, Software, StatisticalMethod |
| Version | 1.30.0 |
| 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_1.30.0.tar.gz |
| Windows Binary | nucleoSim_1.30.0.zip |
| macOS Binary (x86_64) | nucleoSim_1.30.0.tgz |
| macOS Binary (arm64) | nucleoSim_1.30.0.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 |