DOI: 10.18129/B9.bioc.RAREsim  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see RAREsim.

Simulation of Rare Variant Genetic Data

Bioconductor version: 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>

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


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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
Suggests markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0)
URL https://github.com/meganmichelle/RAREsim
BugReports https://github.com/meganmichelle/RAREsim/issues
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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
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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/
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