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ancombc

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

bhglm

BhGLM (Bayesian hierarchical GLMs and survival models)

davidchang

David Chang's periodontal research project

dc-bioc-limma

Differential expression analysis with limma

deseq2

Differential gene expression analysis based on the negative binomial distribution

devis

DEvis: an R package for aggregation and visualization of differential expression data

export

R package for streamlined export of graphs and data tables.

figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

ggpubr

'ggplot2' Based Publication Ready Plots

gmpr

GMPR: A robust normalization method for zero-inflated count data with application to microbiome sequencing data

gneiss

compositional data analysis toolbox

live-demo

maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

managing_batch_effects

melbioinf_docs

Melbourne Bioinformatics documentation in markdown format

metabarpipe

an R package to process raw metabarcoding data into a phyloseq object using a single command

metacoder

Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data

metagenomics-power-analyses-tutorial

Tutorial for doing power analyses for metagenomics.

metalonda

METAgenomic LONgitudinal Differential Abundance method

metaphlan

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

metarna-seq

Custom scripts for creating and annotating multispecies bacterial metagenomes

microbial-bioinformatics-introductory-course-material-2018

Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

microbiomeseq

An R package for microbial community analysis in an environmental context

microbiomeutilities

The is mostly a wrapper tool using phyloseq and microbiome R packages. Apart for some simple scripts, this package has a single function generates a HTML report with preliminary QC, Alpha Diversity, Ordination and Composition analysis of OTU tables.

micropower

power estimation for microbiome studies analyzed with pairwise distances and PERMANOVA

nbzimm

NBZIMM (Negative Binomial and Zero-Inflated Mixed Models)

nbzimm-tutorial

ng-tax

NG-Tax is an improved pipeline for 16S rRNA gene amplicon sequencing data. Several novel steps ensure improved robustness against errors associated with technical aspects of these studies, such as PCR protocols, choice of 16S rRNA gene variable region and variable rates of sequencing error. The commonly reported problems such as many un- or poorly classified OTUs, inflated richness and diversity, taxonomic profiles that do not match the expected ones, region dependent taxonomic classification and results being highly dependent on minor changes in the experimental setup have been tackled with NG-Tax.

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

phylosmith

functions for analyzing phyloseq data