curatedMetagenomicData uses Bioconductor's ExperimentHub to distribute taxonomic and metabolic functional profiles and curated metadata for publicly available human microbiome samples generated by shotgun metagenomic sequencing.
Install curatedMetagenomicData through Bioconductor using BiocManager and
open the
package vignette.
Microbiome profiles and metadata can be accessed from within R or from the
command line.
BiocManager::install("curatedMetagenomicData")
browseVignettes("curatedMetagenomicData")
For more extensive information on installing and using curatedMetagenomicData
please see https://waldronlab.github.io/curatedMetagenomicData/.
Contributions will gladly be accepted provided they fit within the context of the project. Please see CONTRIBUTING.md for information regarding reporting bugs, pull request, adding datasets and other issues.
curatedMetagenomicData is Free software licensed under the Artistic
License 2.0 (copied here as the LICENSE file, verbatim as required by the Perl
Foundation). For the purposes of this license, the "Copyright Holders" are the
authors of the manuscript (https://www.nature.com/articles/nmeth.4468). In
general you may use and re-distribute original and modified versions of the
software under very permissive conditions. The appropriate citation information
for each dataset can be found by doing experimentData(eset) (where eset is
the name of the ExpressionSet class data object), by looking at the man page of
the dataset (e.g. ?HMP_2012), or by looking at the reference manual of the
development
or
release
version.