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.
☆25Dec 10, 2020Updated 5 years ago
Alternatives and similar repositories for AGORA
Users that are interested in AGORA are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno appro…☆70Jul 4, 2026Updated 2 weeks ago
- the toolbox for Microbial and personalized GEM, REactiobiome and community NEtwork modelling☆11Feb 3, 2024Updated 2 years ago
- Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling☆19May 26, 2026Updated last month
- MetScale: snakemake workflows to scale metagenome analyses☆19May 15, 2025Updated last year
- microbiome data simulation package☆22Oct 2, 2025Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- A collection of M models downloaded from published studies☆17Feb 18, 2016Updated 10 years ago
- High-level, high-performance, constraint-based reconstruction and analysis in Julia☆63Apr 26, 2023Updated 3 years ago
- The BiGG Models website server☆91Nov 7, 2019Updated 6 years ago
- CarveMe: genome-scale metabolic model reconstruction☆213Sep 12, 2025Updated 10 months ago
- ☆10Jul 4, 2019Updated 7 years ago
- ☆11Nov 24, 2025Updated 8 months ago
- Pipeline for computing OTU tables from 16S or ITS amplicon sequencing data.☆34Jun 18, 2023Updated 3 years ago
- The standard for open-source GEMs on GitHub☆22Jul 2, 2026Updated 3 weeks ago
- A Python 3 implementation of Thermodynamics-based Flux Analysis☆46Jul 9, 2025Updated last year
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆26Feb 6, 2026Updated 5 months ago
- ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.☆24Jan 28, 2025Updated last year
- Reaction Inclusion by Parsimony and Transcript Distribution☆14Feb 14, 2023Updated 3 years ago
- Metagenomic Analysis☆11Apr 5, 2021Updated 5 years ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆25Jan 24, 2024Updated 2 years ago
- A Qiime plugin for MICOM.☆10Updated this week
- A method for identifying deleterious protein variation.☆11Nov 14, 2016Updated 9 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆32Mar 5, 2019Updated 7 years ago
- memote – the genome-scale metabolic model test suite☆149Aug 14, 2025Updated 11 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- ☆11Mar 10, 2024Updated 2 years ago
- ☆20Mar 31, 2021Updated 5 years ago
- Provides classes for working with sets☆11Dec 19, 2025Updated 7 months ago
- Constraint-based modeling framework for the enumeration of pathway analysis concepts☆14Jul 6, 2023Updated 3 years ago
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆218Jul 13, 2026Updated last week
- A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.☆16Jul 25, 2016Updated 9 years ago
- Genome scale metabolic models in SBML format☆11Nov 16, 2021Updated 4 years ago
- A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets☆13Jul 15, 2026Updated last week
- A Python MPI Pool☆17Jun 21, 2020Updated 6 years ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- A taxonomic classifier for shotgun metagenomics reads☆11Apr 4, 2025Updated last year
- Species richness with high diversity☆68Jun 25, 2026Updated 3 weeks ago
- A pipeline for primary analysis of shotgun metagenomic sequencing data☆11Jun 10, 2019Updated 7 years ago
- Organize & Run Build Scripts Comfortably☆15Apr 21, 2024Updated 2 years ago
- Snakemake workflow to detect and classify viruses in metagenome assemblies.☆19Feb 14, 2024Updated 2 years ago
- Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data☆144Jul 17, 2026Updated last week
- COBRAdb loads genome-scale metabolic models and genome annotations into a relational database. It already powers BiGG Models, and it is a…☆20Oct 29, 2019Updated 6 years ago