metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-metagenomeseq
and update with:
conda update bioconductor-metagenomeseq
A Docker container is available at https://quay.io/repository/biocontainers/bioconductor-metagenomeseq.