A list of R environment based tools for microbiome data exploration, statistical analysis and visualization

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Make Picrust2 Output Analysis and Visualization Easier

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

The Microbial Co-occurrence Network Explorer

iMAP v1.0 (Pre-release): Integrated Microbiome Analysis Pipeline

Hypervariable region primer-based extractor for 16S rRNA and other SSU/LSU sequences.

Sequence based 16S rRNA Taxonomic classifier using MLP

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.

16s rRNA Sequencing Meta-analysis Reproducibility Tool (using mothur).

Fast, accurate taxonomic assignments for the human vaginal microbiota

SCRAPT: An Iterative Algorithm for Clustering Large 16S rRNA Gene Datasets

QIIME2 worklflow. From raw data to a feature table.

The `crest4` python package can automatically assign taxonomic names to DNA sequences obtained from environmental sequencing.

Chemical metrics for microbial communities

MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.

This is an automatic pipeline for analysis of amplicon sequence data including 16S, 18S and ITS. It wraps QIIME commands and complements them with additional analysis where QIIME is not good at, such as combine multiple sequencing runs, OTU clustering and chimeric removal with UP ARSE, alignment filtering with Gblock, removing Chloroplast sequen…

Snakemake template for microbial amplicon sequence analysis with mothur.