57 Open Source Microbiome Software Projects
Free and open source microbiome code projects including engines, APIs, generators, and tools.
Virtualmetabolichuman Agora14 ⭐
The aim of this repository is to maintain, refine, and expand the AGORA collection of genome-scale metabolic reconstructions for human gut microbes through the use of issues. Please note that pull requests will be automatically closed.
Microbiome Analysis Using R15 ⭐
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
Microbial Bioinformatics Introductory Course Material 201822 ⭐
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
Q2 Qemistree20 ⭐
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
16s Rdna V3 V412 ⭐
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Tools for phylogenetic data analysis including visualization and cluster-computing support.
Ancom Bc Code Archive18 ⭐
Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction"
PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
R package for microbiome data visualization. Uses phyloseq, vegan and tidyverse. See website link for docs with visual examples. Docker image available.
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Inference of microbial interaction networks from large-scale heterogeneous abundance data
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data