To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("sparseDOSSA")

In most cases, you don't need to download the package archive at all.

sparseDOSSA

DOI: 10.18129/B9.bioc.sparseDOSSA    

This is the development version of sparseDOSSA; for the stable release version, see sparseDOSSA.

Sparse Data Observations for Simulating Synthetic Abundance

Bioconductor version: Development (3.7)

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")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("sparseDOSSA")

Documentation

HTML R Script Sparse Data Observations for the Simulation of Synthetic Abundances (sparseDOSSA)
PDF   Reference Manual
Text   LICENSE

Details

biocViews Bayesian, Metagenomics, Microbiome, Software
Version 1.3.0
In Bioconductor since BioC 3.5 (R-3.4) (0.5 years)
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  

Package Archives

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

Source Package sparseDOSSA_1.3.0.tar.gz
Windows Binary sparseDOSSA_1.3.0.zip
Mac OS X 10.11 (El Capitan) sparseDOSSA_1.3.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sparseDOSSA
Package Short Url http://bioconductor.org/packages/sparseDOSSA/
Package Downloads Report Download Stats

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