tamascogustavo / chimeraView external linksLinks
Chimera: An easy to use pipeline for Genome based Metabolic Network reconstruction, evaluation and visualization.
☆18Oct 21, 2022Updated 3 years ago
Alternatives and similar repositories for chimera
Users that are interested in chimera are comparing it to the libraries listed below
Sorting:
- Higher-Order Co-occurrence☆12Nov 9, 2021Updated 4 years ago
- mergem is a python package and command-line tool for merging, comparing, and translating genome-scale metabolic models☆13Aug 20, 2025Updated 5 months ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆14Jan 8, 2024Updated 2 years ago
- CarveMe: genome-scale metabolic model reconstruction☆194Sep 12, 2025Updated 5 months ago
- ☆24Oct 11, 2024Updated last year
- ReFramed: metabolic modeling package☆63Sep 16, 2025Updated 5 months ago
- Supplementary data for co-occurrence manuscript☆10Dec 19, 2019Updated 6 years ago
- ☆26Dec 9, 2022Updated 3 years ago
- SMETANA: a tool to analyse interactions in microbial communities☆66May 6, 2025Updated 9 months ago
- Inference of microbial interaction networks from large-scale heterogeneous abundance data☆90Oct 9, 2025Updated 4 months ago
- Beta-Poisson model for single-cell RNA-seq data analyses☆16Feb 8, 2019Updated 7 years ago
- Automated synthetic microbial Community Design☆13Mar 26, 2021Updated 4 years ago
- Biological Pathway Visualization☆11Apr 8, 2021Updated 4 years ago
- ☆11Jun 12, 2024Updated last year
- Pipelines used in the lab.☆15Mar 26, 2025Updated 10 months ago
- agent based modelling☆34Aug 28, 2024Updated last year
- An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within micro…☆254Jul 27, 2024Updated last year
- Drawing 'dendrogram' using 'ggtree'☆13Nov 1, 2025Updated 3 months ago
- Python package to study microbial communities using metabolic modeling.☆115Jan 26, 2026Updated 3 weeks ago
- A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML…☆20Jun 26, 2023Updated 2 years ago
- Qiime2 snakemake pipeline☆20Dec 21, 2023Updated 2 years ago
- A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard f…☆16Jul 9, 2025Updated 7 months ago
- A newly developed metabolic modeling pipeline, SuperCC, which could simulate the performances of different microbiomes.☆25Nov 21, 2025Updated 2 months ago
- an R package for deep mining gene co-expression networks in multi-trait expression data☆21Jan 23, 2026Updated 3 weeks ago
- 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
- BRENDA parser in python☆22May 16, 2022Updated 3 years ago
- Repository of tutorials for The COBRA Toolbox☆24Feb 6, 2026Updated last week
- Template for building a bioconductor workshop package using github actions☆21Jun 26, 2025Updated 7 months ago
- An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuris…☆24Dec 4, 2025Updated 2 months ago
- tidyMicro GitHup Repository☆21Nov 17, 2021Updated 4 years ago
- Teaching materials for cobrapy, cameo, escher and DD-DeCaF☆26Jul 12, 2022Updated 3 years ago
- memote – the genome-scale metabolic model test suite☆144Aug 14, 2025Updated 6 months ago
- A Shiny web server for interactive visualization and analysis of RNA-seq data☆22Mar 24, 2021Updated 4 years ago
- Parse NCBI CD-search results to find and visualise the domain architecture of secondary metabolite synthases☆24Nov 9, 2022Updated 3 years ago
- ☆24Oct 19, 2023Updated 2 years ago
- ☆23Aug 28, 2020Updated 5 years ago
- An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced feat…☆62Dec 22, 2025Updated last month
- Ready-made Taxonomic Weights Repository☆26Mar 31, 2022Updated 3 years ago
- MAGinator - Accurate SNV calling and profiling of MAGs☆26May 21, 2025Updated 8 months ago