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Extensions for the phyloseq package for R

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See the index of included extensions To browse the output of the extension examples, or quickly grab the extension function code from the top of the example. Please heed the request for citing this work if you find it useful. Each extension tutorial lists the relevant publications that should be cited.

This is a repository of self-contained extensions for the phyloseq package for R. Typically these extensions are provided here because they rely on a separate R package that is not among the official dependencies in phyloseq, but may still be useful in special cases.

If you find any of this code useful, please cite the publication describing phyloseq (below), as well as any additional citations mentioned in the extension's tutorial. The source code for creating each tutorial is also provided in this repository as R-flavored markdown.

Citing phyloseq:

McMurdie and Holmes (2013) phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 8(4):e61217