Bioconductor version: Release (3.6)
The package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA's model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most importantly, it allows users to include both known feature-feature and feature-metadata correlation structures and thus provides a gold standard to enable benchmarking of statistical methods for metagenomic data analysis.
Author: Boyu Ren<bor158 at mail.harvard.edu>, Emma Schwager<emma.schwager at gmail.com>, Timothy Tickle<ttickle at hsph.harvard.edu>, Curtis Huttenhower <chuttenh at hsph.harvard.edu>
Maintainer: Boyu Ren<bor158 at mail.harvard.edu>, Emma Schwager <emma.schwager at gmail.com>, George Weingart<george.weingart at gmail.com>
Citation (from within R,
enter citation("sparseDOSSA")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("sparseDOSSA")
HTML | R Script | Sparse Data Observations for the Simulation of Synthetic Abundances (sparseDOSSA) |
Reference Manual | ||
Text | LICENSE |
biocViews | Bayesian, Metagenomics, Microbiome, Software |
Version | 1.2.0 |
In Bioconductor since | BioC 3.5 (R-3.4) (1 year) |
License | MIT + file LICENSE |
Depends | |
Imports | stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack |
LinkingTo | |
Suggests | knitr, BiocStyle, BiocGenerics, rmarkdown |
SystemRequirements | |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | sparseDOSSA_1.2.0.tar.gz |
Windows Binary | sparseDOSSA_1.2.0.zip |
Mac OS X 10.11 (El Capitan) | sparseDOSSA_1.2.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/sparseDOSSA |
Package Short Url | http://bioconductor.org/packages/sparseDOSSA/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: