sparseDOSSA

DOI: 10.18129/B9.bioc.sparseDOSSA    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see sparseDOSSA.

Sparse Data Observations for Simulating Synthetic Abundance

Bioconductor version: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("sparseDOSSA")

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("sparseDOSSA")

 

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

Details

biocViews	Bayesian, ImmunoOncology, Metagenomics, Microbiome, Software
Version	1.6.1
In Bioconductor since	BioC 3.5 (R-3.4) (2 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
Links To Me
Build Report

Package Archives

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

Source Package	sparseDOSSA_1.6.1.tar.gz
Windows Binary	sparseDOSSA_1.6.1.zip
Mac OS X 10.11 (El Capitan)	sparseDOSSA_1.6.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sparseDOSSA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sparseDOSSA
Package Short Url	http://bioconductor.org/packages/sparseDOSSA/
Package Downloads Report	Download Stats