RAREsim
Simulation of Rare Variant Genetic Data
Bioconductor version: Release (3.19)
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("RAREsim")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Genetics, Sequencing, Software, VariantAnnotation |
| Version | 1.8.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
See More
| Suggests | markdown, ggplot2, BiocStyle, rmarkdown, knitr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RAREsim_1.8.0.tar.gz |
| Windows Binary (x86_64) | RAREsim_1.8.0.zip (64-bit only) |
| macOS Binary (x86_64) | RAREsim_1.8.0.tgz |
| macOS Binary (arm64) | RAREsim_1.8.0.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 |