pico: an R package that provides a suite of compositional data analysis (CoDA) functions targeted for marker gene (16S/18S, etc.) microbiome datasets (though really applicable to any n x p count matrix).
Affiliated manuscript: The associated manuscript is in preparation but parts of the package were used for analysis in:
Brown BP, Jaspan HB. Compositional analyses reveal correlations between taxon-level gut bacterial abundance and peripheral T cell marker expression in African infants. Gut microbes. 2019 Jul 28:1-8. PMID31347944
Package will be available via Bioconductor shortly.
microfiltR: an R package that aims to identify and mitigate exogenous- and cross-contamination in compositional marker gene (16S/18S, etc.) surveys.
Affiliated manuscript: The associated manuscript is in preparation but parts of the package were used for analysis in:
Brown BP, Wendoh J, Chopera D, Havyarimana E, Jaumdally SZ, Nyangahu DD, Gray C, Martin DP, Varsani A, Jaspan HB. crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyads. bioRxiv. 2019 Jan 1:582015.
marker gene dataset merging functions: a collection of R functions that provide several statistical transformations and standardizations for the merging of marker gene datasets (16S/18S, etc.) while accurately preserving relative ratios of taxa across datasets. Compatible with phyloseq-class datasets.
assorted CoDA functions: a repository of R functions and code for the compositional analysis of count data in an n x p matrix