nucleoSim
Generate synthetic nucleosome maps
Bioconductor version: Release (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("nucleoSim")
):
Installation
To install this package, start R (version "4.4") 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 | 1.32.0 |
In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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 |
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_1.32.0.tar.gz |
Windows Binary | nucleoSim_1.32.0.zip |
macOS Binary (x86_64) | nucleoSim_1.32.0.tgz |
macOS Binary (arm64) | nucleoSim_1.32.0.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 |