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agora

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.

ancient-microbiome-denovo

api

Website holding MSDK API

bile_acid_ad

biobakery

bioBakery tools for meta'omic profiling

biodatascience

This is the web resource for NTU's Bio-Data Science and Education Laboratory

cerosaletti_linsley

cobra.tutorials

Repository of tutorials for The COBRA Toolbox

cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox

codebase

Code depository for papers

compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes

context_specific_models_from_gems

A systematic evaluation of methods for tailoring genome-scale metabolic models

cy2fluxviz

deepmet

deviumweb

Interactive multivariate data analysis in R implemented in shiny.

diab_gsmm_t1d

Scripts for data analysis and GSMM – Diabimmune T1D study

export2graphlan

Conversion software tool for producing both annotation and tree files for GraPhlAn

freecodecamp-pandas-real-life-example

gmms

A manually curated database of human gut metabolic modules.

groningen-microbiome

Microbiome Projects from the Department of Genetics and Department of Gastroenterology and Hepatology , University Medical Centre Groningen

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

humann

HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).

irfinder

Scheduled for testing

isls9

iSLS9 data analysis workshop

iso2flux

lefse

matplotlib

matplotlib: plotting with Python

metabolomics2019

Tutorials

metadeconfoundr

metamapr

Network mapping tool for metabolomics + data.