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sparseDOSSA

Sparse Data Observations for Simulating Synthetic Abundance


Bioconductor version: Release (3.18)

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 (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sparseDOSSA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Bayesian, ImmunoOncology, Metagenomics, Microbiome, Software
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License MIT + file LICENSE
Depends
Imports stats, utils, optparse, MASS, tmvtnorm (>= 1.4.10), MCMCpack
System Requirements
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Suggests knitr, BiocStyle, BiocGenerics, rmarkdown
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Package Archives

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

Source Package
Windows Binary sparseDOSSA_1.26.0.zip
macOS Binary (x86_64) sparseDOSSA_1.26.0.tgz
macOS Binary (arm64) sparseDOSSA_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sparseDOSSA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sparseDOSSA
Bioc Package Browser https://code.bioconductor.org/browse/sparseDOSSA/
Package Short Url https://bioconductor.org/packages/sparseDOSSA/
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