fionarhuang / microbiomeexperiment

Bioconductor defining a SummarizedExperiment class for microbiome data

MicrobiomeExperiment

This project is aimed to provide a SummarizedExperiment infrastructure for microbiome experiment data. It is based on the TreeSummarizedExperiment package and adds additional functionality from the microbiome analysis world to the context of working with SummarizedExperiment.

Currently this includes:

• recognition of taxonomic information in rowData
• row and column merging
• agglomeration by taxonomic information (like phyloseq)

ToDo

In this package

• addition of reference sequences slots
• addition of specialized taxonomic container, if necessary
• ...

In other packages

• alpha and beta diversity measure (Mia)
• plotting functions
• ...

Contribution

Feel free to contribute.

Technical aspects

Let's use a git flow kind of approach. Development version should be done against the master branch and then merged to release for release. (https://guides.github.com/introduction/flow/)

Code of conduct

Please note that the MicrobiomeExperiment project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.