https://github.com/blekhmanlab/MicroBioMap
R package for fetching and parsing data of the Human Microbiome Compendium
https://github.com/blekhmanlab/MicroBioMap
bioinformatics microbiome microbiome-data rstats taxonomy
Last synced: about 1 year ago
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R package for fetching and parsing data of the Human Microbiome Compendium
- Host: GitHub
- URL: https://github.com/blekhmanlab/MicroBioMap
- Owner: blekhmanlab
- License: other
- Created: 2023-07-12T20:55:04.000Z (almost 3 years ago)
- Default Branch: devel
- Last Pushed: 2025-01-24T21:33:59.000Z (over 1 year ago)
- Last Synced: 2025-03-21T00:32:59.505Z (about 1 year ago)
- Topics: bioinformatics, microbiome, microbiome-data, rstats, taxonomy
- Language: R
- Homepage: https://blekhmanlab.github.io/MicroBioMap/
- Size: 6.78 MB
- Stars: 9
- Watchers: 6
- Forks: 4
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Microbiome Compendium
Our dataset includes more than 168,000 samples of publicly available 16S rRNA
amplicon sequencing data, all processed using the same pipeline and reference
database.
The goal of the MicroBioMap package is simply to expose these data
to the broad community of Bioconductor and R users with
the smallest fuss possible.
See the [vignette](https://seandavi.github.io/MicroBioMap/articles/overview.html) for more details.
## Installation
For the smoothest installation experience, use the [`BiocManager` Bioconductor
package](https://bioconductor.org/packages/BiocManager).
```
BiocManager::install('seandavi/MicroBioMap')
```
## Usage
Load the compendium using:
```
library(MicroBioMap)
cpd <- getCompendium()
```
The resulting object is a `TreeSummarizedExperiment` object. Currently, the
"tree" part of the TreeSummarizedExperiment is not populated, but that is
on the roadmap.
After loading the compendium, you will have immediate access to nearly
170,000 microbiome samples.
The `getCompendium` function retrieves [data stored by Zenodo](https://doi.org/10.5281/zenodo.8186993) and accepts an optional parameter indicating which version to download—for example, `getCompendium('1.0.1')`. Version 1.0.1 is retrieved by default.