RAREsim

DOI: 10.18129/B9.bioc.RAREsim  

Simulation of Rare Variant Genetic Data

Bioconductor version: Release (3.17)

Haplotype simulations of rare variant genetic data that emulates real data can be performed with RAREsim. RAREsim uses the expected number of variants in MAC bins - either as provided by default parameters or estimated from target data - and an abundance of rare variants as simulated HAPGEN2 to probabilistically prune variants. RAREsim produces haplotypes that emulate real sequencing data with respect to the total number of variants, allele frequency spectrum, haplotype structure, and variant annotation.

Author: Megan Null [aut], Ryan Barnard [cre]

Maintainer: Ryan Barnard <rbarnard1107 at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("RAREsim")

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("RAREsim")

 

HTML	R Script	RAREsim Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Genetics, Sequencing, Software, VariantAnnotation
Version	1.4.0
In Bioconductor since	BioC 3.15 (R-4.2) (1.5 years)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	nloptr
LinkingTo
Suggests	markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL	https://github.com/meganmichelle/RAREsim
BugReports	https://github.com/meganmichelle/RAREsim/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RAREsim_1.4.0.tar.gz
Windows Binary	RAREsim_1.4.0.zip
macOS Binary (x86_64)	RAREsim_1.4.0.tgz
macOS Binary (arm64)	RAREsim_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RAREsim
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RAREsim
Bioc Package Browser	https://code.bioconductor.org/browse/RAREsim/
Package Short Url	https://bioconductor.org/packages/RAREsim/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive