This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see metagenomeFeatures.
Bioconductor version: 3.8
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 (from within R,
enter citation("metagenomeFeatures")
):
To install this package, start R (version "3.5") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("metagenomeFeatures")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("metagenomeFeatures")
HTML | R Script | `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. |
Reference Manual | ||
Text | NEWS |
biocViews | Annotation, ImmunoOncology, Infrastructure, Metagenomics, Microbiome, Sequencing, Software |
Version | 2.2.3 |
In Bioconductor since | BioC 3.2 (R-3.2) (3.5 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) |
LinkingTo | |
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) |
SystemRequirements | |
Enhances | |
URL | https://github.com/HCBravoLab/metagenomeFeatures |
BugReports | https://github.com/HCBravoLab/metagenomeFeatures/issues |
Depends On Me | |
Imports Me | greengenes13.5MgDb, ribosomaldatabaseproject11.5MgDb, silva128.1MgDb |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | metagenomeFeatures_2.2.3.tar.gz |
Windows Binary | metagenomeFeatures_2.2.3.zip |
Mac OS X 10.11 (El Capitan) | metagenomeFeatures_2.2.3.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/metagenomeFeatures |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/metagenomeFeatures |
Package Short Url | http://bioconductor.org/packages/metagenomeFeatures/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: