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RAREsim

Simulation of Rare Variant Genetic Data


Bioconductor version: Release (3.18)

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>

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

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")
RAREsim Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Genetics, Sequencing, Software, VariantAnnotation
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.1.0)
Imports nloptr
System Requirements
URL https://github.com/meganmichelle/RAREsim
Bug Reports https://github.com/meganmichelle/RAREsim/issues
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Suggests markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
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Package Archives

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

Source Package RAREsim_1.6.0.tar.gz
Windows Binary RAREsim_1.6.0.zip
macOS Binary (x86_64) RAREsim_1.6.0.tgz
macOS Binary (arm64) RAREsim_1.6.0.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