microbiomeDASim
This is the released version of microbiomeDASim; for the devel version, see microbiomeDASim.
Microbiome Differential Abundance Simulation
Bioconductor version: Release (3.23)
A toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.
Author: Justin Williams, Hector Corrada Bravo, Jennifer Tom, Joseph Nathaniel Paulson
Maintainer: Justin Williams <williazo at ucla.edu>
citation("microbiomeDASim")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("microbiomeDASim")
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("microbiomeDASim")| microbiomeDASim | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Microbiome, Software, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.6.0) |
| Imports | graphics, ggplot2, MASS, tmvtnorm, Matrix, mvtnorm, pbapply, stats, phyloseq, metagenomeSeq, Biobase |
| System Requirements | |
| URL | https://github.com/williazo/microbiomeDASim |
| Bug Reports | https://github.com/williazo/microbiomeDASim/issues |
See More
| Suggests | testthat (>= 2.1.0), knitr, devtools |
| 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 | microbiomeDASim_1.26.0.tar.gz |
| Windows Binary (x86_64) | microbiomeDASim_1.26.0.zip |
| macOS Binary (big-sur-x86_64) | microbiomeDASim_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | microbiomeDASim_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/microbiomeDASim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/microbiomeDASim |
| Bioc Package Browser | https://code.bioconductor.org/browse/microbiomeDASim/ |
| Package Short Url | https://bioconductor.org/packages/microbiomeDASim/ |
| Package Downloads Report | Download Stats |