metagenomeFeatures
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see metagenomeFeatures .
Exploration of marker-gene sequence taxonomic annotations
Bioconductor version: 3.9
metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.
Author: Nathan D. Olson, Joseph Nathaniel Paulson, Hector Corrada Bravo
Maintainer: Nathan D. Olson <nolson at umiacs.umd.edu>
citation("metagenomeFeatures")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("metagenomeFeatures")
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("metagenomeFeatures")| `metagenomeFeatures` classes and methods. | HTML | R Script |
| Exploring sequence and phylogenetic diversity for a taxonomic group of interest. | HTML | R Script |
| Using metagenomeFeatures to Retrieve Feature Data. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software |
| Version | 2.4.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (8.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5), Biobase(>= 2.17.8) |
| Imports | Biostrings(>= 2.36.4), S4Vectors(>= 0.14.7), dplyr (>= 0.7.0), dbplyr (>= 1.0.0), stringr (>= 1.0.0), lazyeval (>= 0.1.10), RSQLite (>= 1.0.0), magrittr (>= 1.5), methods (>= 3.3.1), lattice (>= 0.20.33), ape (>= 3.5), DECIPHER(>= 2.4.0) |
| System Requirements | |
| URL | https://github.com/HCBravoLab/metagenomeFeatures |
| Bug Reports | https://github.com/HCBravoLab/metagenomeFeatures/issues |
See More
| Suggests | knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), devtools (>= 1.13.5), ggtree(>= 1.8.2), BiocStyle(>= 2.8.2), phyloseq(>= 1.24.2), forcats (>= 0.3.0), ggplot2 (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | metagenomeFeatures_2.4.0.tar.gz |
| Windows Binary | metagenomeFeatures_2.4.0.zip |
| Mac OS X 10.11 (El Capitan) | metagenomeFeatures_2.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/metagenomeFeatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagenomeFeatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/metagenomeFeatures/ |
| Package Short Url | https://bioconductor.org/packages/metagenomeFeatures/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |