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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")
In most cases, you don't need to download the package archive at all.
metagenomeSeq
|
This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see metagenomeSeq.
Statistical analysis for sparse high-throughput sequencing
Bioconductor version: 3.4
metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
Author: Joseph Nathaniel Paulson, Hisham Talukder, Mihai Pop, Hector Corrada Bravo
Maintainer: Joseph N. Paulson <jpaulson at jimmy.harvard.edu>
Citation (from within R,
enter citation("metagenomeSeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("metagenomeSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagenomeSeq")
| R Script | fitTimeSeries: differential abundance analysis through time or location | |
| R Script | metagenomeSeq: statistical analysis for sparse high-throughput sequencing | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Normalization, Sequencing, Software, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0), Biobase, limma, glmnet, methods, RColorBrewer |
| Imports | parallel, matrixStats, foreach, Matrix, gplots |
| LinkingTo | |
| Suggests | annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/nosson/metagenomeSeq/ |
| BugReports | https://github.com/nosson/metagenomeSeq/issues |
| Depends On Me | etec16s, msd16s |
| Imports Me | metagenomeFeatures |
| Suggests Me | interactiveDisplay, phyloseq |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | metagenomeSeq_1.16.0.tar.gz |
| Windows Binary | metagenomeSeq_1.16.0.zip |
| Mac OS X 10.9 (Mavericks) | metagenomeSeq_1.16.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/metagenomeSeq/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/metagenomeSeq/ |
| Package Downloads Report | Download Stats |
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