A tool for representing genomic potential and transcriptomic expression into KEGG pathways
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Jul 28, 2024 - Python
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metabolic-pathways
Here are 15 public repositories matching this topic...
scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.
systems-biology metabolism single-cell metabolic-pathways spatial-transcriptomics single-cell-transcriptomics metabolic-modeling
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Sep 3, 2025 - Python
🤝 Tool for mining KEGG pathways completeness data from eggNOG-mapper annotations
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Oct 18, 2025 - Python
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
bioinformatics synthetic-biology systems-biology computational-biology python3 simulation-toolkit modeling-tool metabolic-models metabolic-engineering metabolic-pathways
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Nov 4, 2025 - Python
Identifying reprogrammed metabolic routes given omics data.
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Dec 2, 2022 - Python
Library to perform metabolic engineering tasks
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Apr 29, 2024 - Python
Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc
bioinformatics taxonomy hpc uniprot unh metabolic-pathways paladin protein-alignment nucleotide-alignment
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Apr 13, 2024 - Python
reMap: relabeling metabolic pathway data with groups to improve prediction outcomes
groups bioinformatics embeddings topic-modeling multi-label-classification bags centroid multi-label-learning metacyc metabolic-pathways relabel biocyc bags-of-pathways pathway2vec groups-of-pathways
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Nov 8, 2021 - Python
prepBioCyc: Preprocess BioCyc files
bioinformatics graph metagenomics bioinformatics-pipeline heterogeneous-network data-wrangling bioinformatics-analysis metabolic-network metacyc metabolic-pathways bioinformatics-tool biocyc
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Apr 27, 2022 - Python
Metabolic pathway inference using non-negative matrix factorization with community detection
bioinformatics community-detection metagenomics multi-label-classification metabolic-reconstruction non-negative-matrix-factorization multi-label-learning pathway-prediction metacyc metabolic-pathways subnetwork biocyc pathway2ec-association-matrix
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Sep 19, 2021 - Python
Serves as the backend code for https://www.curatemetabolicpathways.com
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Apr 26, 2021 - Python
leADS: improved metabolic pathway inference based on active dataset subsampling
bioinformatics metagenomics metabolic-network multi-label-learning multi-label-classfications metacyc metabolic-pathways acquisition-functions biocyc pathway-tools multi-label-imbalance active-dataset-subsampling metabolic-pathway-prediction
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Nov 16, 2021 - Python
python bioinformatics computational-biology constraint-based-modeling metabolic-pathways stoichiometric-modeling
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Mar 12, 2025 - Python
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
bioinformatics metagenomics topic-modeling pathway-analysis metabolic-network metabolic-reconstruction pathway-prediction metacyc metabolic-pathways pathway-enrichment-analysis pathway-reconstruction biocyc pathway-tools
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Nov 8, 2021 - Python
Code and data repository for Modeling Metabolic Fluxes Using Deep Learning Based on Enzyme Variations
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Dec 14, 2024 - Python
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