NOTE While we continue to maintain this R package, the development has been discontinued as we have shifted to supporting methods development based on the new TreeSummarizedExperiment data container, which provides added capabilities for multi-omics data analysis. Check the miaverse project for details.
We recommend switching from phyloseq to the TreeSummarizedExperiment based methods described in the Orchestrating Microbiome Analysis (OMA) online book, which is where method development now takes place.
To ease that transition, most functions in this package now accept
TreeSummarizedExperiment (and other SummarizedExperiment-derived)
objects in addition to phyloseq objects. Two things are worth noting.
Functions that manipulate the taxonomy table (aggregate_taxa,
plot_composition, map_levels, psmelt2, the tibble utilities and
the read_* family) remain phyloseq only. And for a
TreeSummarizedExperiment, transform() follows the mia convention
of storing its result as a new named assay rather than overwriting the
counts, so the result is read back with
abundances(x, assay.type = "clr") rather than abundances(x).
Tools for the exploration and analysis of microbiome profiling data sets.
This R package extends the phyloseq data container, and also supports the (Tree)SummarizedExperiment containers. We have discontinued the development and shifted to support methods development based on the (Tree)SummarizedExperiment data containers, see microbiome.github.io for more details.
See the package tutorial.
Kindly cite as follows: Sudarshan Shetty and Leo Lahti. Journal of Biosciences 44(5):115, 2019. doi: 10.1007/s12038-019-9930-2
Main developer: Leo Lahti
Main co-authors: Sudarshan Shetty
Thanks for [@johanneskoester] and [@nick-youngblut] for contributing Bioconda installation recipe.
The work has been supported by the following bodies:
This work extends the independent phyloseq package and data structures for R-based microbiome analysis.