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DirichletMultinomial
Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data
Bioconductor version: 3.0
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.
Author: Martin Morgan <mtmorgan at fhcrc.org>
Maintainer: Martin Morgan <mtmorgan at fhcrc.org>
Citation (from within R,
enter citation("DirichletMultinomial")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DirichletMultinomial")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DirichletMultinomial")
| An introduction to DirichletMultinomial | ||
| Reference Manual |
Details
| biocViews | Classification, Clustering, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | LGPL-3 |
| Depends | S4Vectors, IRanges |
| Imports | stats4, methods |
| LinkingTo | |
| Suggests | lattice, parallel, MASS, RColorBrewer, xtable |
| SystemRequirements | gsl |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | TFBSTools |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DirichletMultinomial_1.8.0.tar.gz |
| Windows Binary | DirichletMultinomial_1.8.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DirichletMultinomial_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | DirichletMultinomial_1.8.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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