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amon

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

atlas

ATLAS - Three commands to start analysing your metagenome data

bioconda-recipes

Conda recipes for the bioconda channel.

cloud-genomics

datacodes_iomicspass

gem

Build your own GEM model

h5py

HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

hydra

Pipeline for amplicon sequencing projects. OTUs can be build with various methods (usearch,vsearch,uparse,swarm) and classified using the RDP Classifier and SINA. Final output is a BIOM file for downstream processing (Phyloseq/R)

kraken2

The second version of the Kraken taxonomic sequence classification system

microbiomeqtl

A pipeline for microbiome analysis

mzmine2

MZmine 2 source code repository

omics

Codes of the statistical analyses using for "an aberrant intestinal microbiota aggravates renal failure in human and rodents".

picrust2

Code, unit tests, and tutorials for running PICRUSt2

picrust_galaxy

Create a galaxy instance of PICRUSt.

qc-ngs

This tutorial will guide you through the process of generating and reading a QC report.

training-material

A collection of Galaxy-related training material

trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly

worldmap-panel

Worldmap panel plugin for Grafana 3.0 that can be overlaid with circles for data points.