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.
☆24Dec 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:
- the toolbox for Microbial and personalized GEM, REactiobiome and community NEtwork modelling☆11Feb 3, 2024Updated 2 years ago
- MetScale: snakemake workflows to scale metagenome analyses☆19May 15, 2025Updated 10 months ago
- microbiome data simulation package☆22Oct 2, 2025Updated 5 months ago
- A collection of M models downloaded from published studies☆16Feb 18, 2016Updated 10 years ago
- The BiGG Models website server☆88Nov 7, 2019Updated 6 years ago
- Taxallnomy is a balanced taxonomic tree database based on NCBI Taxonomy that provides taxonomic lineages according to the taxonomic ranks…☆13Apr 13, 2025Updated 11 months ago
- High-level, high-performance, constraint-based reconstruction and analysis in Julia☆63Apr 26, 2023Updated 2 years ago
- ☆10Jul 4, 2019Updated 6 years ago
- CarveMe: genome-scale metabolic model reconstruction☆198Sep 12, 2025Updated 6 months ago
- Scripts to build high-quality genome-scale metabolic model by using a deep neural network to guide gapfilling☆18Mar 18, 2025Updated last year
- ☆10Nov 24, 2025Updated 4 months ago
- The standard for open-source GEMs on GitHub☆21Oct 26, 2023Updated 2 years ago
- ☆13Feb 29, 2024Updated 2 years ago
- A Python 3 implementation of Thermodynamics-based Flux Analysis☆43Jul 9, 2025Updated 8 months ago
- ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.☆23Jan 28, 2025Updated last year
- This repository contains all source code in the reconstructor python package, installation instructions, important file dependencies, and…☆24Feb 6, 2026Updated last month
- Metagenomic Analysis☆11Apr 5, 2021Updated 4 years ago
- Reaction Inclusion by Parsimony and Transcript Distribution☆12Feb 14, 2023Updated 3 years ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆24Jan 24, 2024Updated 2 years ago
- A method for identifying deleterious protein variation.☆11Nov 14, 2016Updated 9 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆30Mar 5, 2019Updated 7 years ago
- LaTeX template of graduate Thesis [University of Chinese Academy of Sciences]☆12Nov 7, 2017Updated 8 years ago
- The seqtime R package provides functions to analyse sequencing data time series and to simulate community dynamics☆21Dec 9, 2022Updated 3 years ago
- ☆11Mar 10, 2024Updated 2 years ago
- ☆20Mar 31, 2021Updated 4 years ago
- Provides classes for working with sets☆11Dec 19, 2025Updated 3 months ago
- memote – the genome-scale metabolic model test suite☆145Aug 14, 2025Updated 7 months ago
- Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks☆206Mar 5, 2026Updated 2 weeks ago
- A cookiecutter template that reflects my favored structure for setting up Snakemake-based analysis pipelines.☆16Jul 25, 2016Updated 9 years ago
- A Python MPI Pool☆17Jun 21, 2020Updated 5 years ago
- Genome scale metabolic models in SBML format☆10Nov 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☆13Updated this week
- 🖨️ Print pictures with living micro-organisms!☆14Apr 9, 2025Updated 11 months ago
- A taxonomic classifier for shotgun metagenomics reads☆11Apr 4, 2025Updated 11 months ago
- Species richness with high diversity☆68Aug 5, 2025Updated 7 months ago
- Constraint-based modeling framework for the enumeration of pathway analysis concepts☆14Jul 6, 2023Updated 2 years ago
- A python library for metabolic networks sampling and analysis☆67Feb 4, 2026Updated last month
- Snakemake workflow to detect and classify viruses in metagenome assemblies.☆19Feb 14, 2024Updated 2 years ago
- A pipeline for primary analysis of shotgun metagenomic sequencing data☆11Jun 10, 2019Updated 6 years ago