sparseDOSSA
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see sparseDOSSA.
Sparse Data Observations for Simulating Synthetic Abundance
Bioconductor version: 3.11
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("sparseDOSSA")):
Installation
To install this package, start R (version "4.0") 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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sparseDOSSA")| Sparse Data Observations for the Simulation of Synthetic Abundances (sparseDOSSA) | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Bayesian, ImmunoOncology, Metagenomics, Microbiome, Software |
| Version | 1.12.0 |
| 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 | |
| URL |
See More
| Suggests | knitr, BiocStyle, BiocGenerics, rmarkdown |
| 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 | sparseDOSSA_1.12.0.tar.gz |
| Windows Binary | sparseDOSSA_1.12.0.zip |
| macOS 10.13 (High Sierra) | sparseDOSSA_1.12.0.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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.11 | Source Archive |