Supplementary data for co-occurrence manuscript
☆10Dec 19, 2019Updated 6 years ago
Alternatives and similar repositories for cooccurrence
Users that are interested in cooccurrence are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Higher-Order Co-occurrence☆12Nov 9, 2021Updated 4 years ago
- SMETANA: a tool to analyse interactions in microbial communities☆67May 6, 2025Updated 11 months ago
- Gupta et al., TaxiBGC: a Taxonomy-guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Sec…☆15May 24, 2023Updated 2 years ago
- EMBL GEMs: A collection of GEnome-scale Models for bacterial species☆30Mar 5, 2019Updated 7 years ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆14Jan 8, 2024Updated 2 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Pipelines used in the lab.☆15Mar 26, 2025Updated last year
- agent based modelling☆35Aug 28, 2024Updated last year
- Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.☆18Oct 21, 2022Updated 3 years ago
- Python package to study microbial communities using metabolic modeling.☆124Mar 31, 2026Updated last week
- Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publicatio…☆13Jan 14, 2023Updated 3 years ago
- tool for dating gene age by micro- and macro-synteny with high speed and accuracy☆15Jan 3, 2026Updated 3 months ago
- MGnify API toolkit☆19Jan 31, 2025Updated last year
- BiGMeC - Biosynthetic Gene cluster Metabolic pathway Constructor☆16May 14, 2023Updated 2 years ago
- microbial association network clustering algorithm☆14Dec 14, 2023Updated 2 years ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A pipeline for the identification of fungi in public metagenomics datasets☆17Nov 23, 2020Updated 5 years ago
- Enzyme-constrained genome-scale models in python☆37Oct 25, 2023Updated 2 years ago
- ☆18Dec 11, 2024Updated last year
- Database of genomes integrated from the gut microbiome and other environments☆45Feb 3, 2023Updated 3 years ago
- ☆20Dec 15, 2020Updated 5 years ago
- The Microbial Co-occurrence Network Explorer☆21Oct 17, 2023Updated 2 years ago
- Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.☆18Jan 7, 2026Updated 3 months ago
- Analysing Metagenomic Species (MGS)☆42Nov 12, 2020Updated 5 years ago
- From annotated genomes to metabolic screening in large scale microbiotas☆71Mar 26, 2026Updated 2 weeks ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Python interface for running COMETS simulations and analyzing the results☆16Feb 24, 2026Updated last month
- Automatic eukaryotic taxonomic classification☆29May 9, 2025Updated 11 months ago
- Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction☆16Jul 8, 2021Updated 4 years ago
- ☆24Dec 5, 2018Updated 7 years ago
- A gene-targeted assembler tool☆19Oct 27, 2017Updated 8 years ago
- CarveMe: genome-scale metabolic model reconstruction☆199Sep 12, 2025Updated 6 months ago
- Metabolic Engineering Workbench☆41Jun 9, 2024Updated last year
- ☆20Mar 29, 2022Updated 4 years ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆91Oct 9, 2025Updated 6 months ago
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Constraint-Based Reconstruction and EXascale Analysis☆46Oct 23, 2024Updated last year
- ☆47Jun 11, 2025Updated 10 months ago
- Knowledge-based Identification of Pathway Enzymes (KIPEs) performs an automatic annotation of the flavonoid biosynthesis steps in a new t…☆17Feb 12, 2026Updated 2 months ago
- The dysbiosisR package implements tools for calculating some common microbiome dysbiosis measures☆15Dec 2, 2022Updated 3 years ago
- GEne Cluster prediction with COnditional random fields.☆84Mar 10, 2026Updated last month
- A visualization tool for Systems-Level Interactive Data Exploration☆12Jan 12, 2022Updated 4 years ago
- Predicting biosynthetic gene clusters in genomes☆42Nov 26, 2013Updated 12 years ago