microbiome topic

The is mostly a wrapper tool using phyloseq and microbiome R packages.

microsud

For analysis of microbiome and microbial community data

EcoJulia

Compare different differential abundance and expression methods

Russel88

Various functions for analysis of microbial community data

Russel88

creating hybrid-gene phylogenetic trees for diversity analyses

JTFouquier

A tool for agile functional analysis of shotgun metagenomic data

metageni

Differential analysis of multi-omics data based on the Tweedie distribution

himelmallick

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.

david-barnett

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

nextgenusfs

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

biobakery