Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
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Dec 5, 2024 - R
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metabolic-pathways
Here are 26 public repositories matching this topic...
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
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Jul 28, 2024 - Python
Infer metabolic directions from moment differences of mass-weighted intensity distributions
annotations moment metabolomics mass-spectrometry moments metabolic-models metabolic-network metabolic-engineering mass-spectrum metabolic-pathways metabolic-flux-analysis mass-spectra mass-spectrometry-data metabolic-networks
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Feb 9, 2024 - R
Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
api rest-api genbank blast metabolomics uniprot metabolic-network metabolic-engineering chembl metabolic-pathways rhea
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Dec 12, 2023 - Go
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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Jan 10, 2025 - Python
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Feb 17, 2023 - Jupyter Notebook
Identifying reprogrammed metabolic routes given omics data.
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Dec 2, 2022 - Python
Diversity-based enumeration of optimal context-specific metabolic networks
optimization metabolism metabolic-network metabolic-reconstruction constraint-based-modeling metabolic-engineering cobra-toolbox omics-data-integration metabolic-pathways
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Jul 2, 2021 - MATLAB
Library to perform metabolic engineering tasks
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Apr 29, 2024 - Python
scCellFie offers advanced analysis of metabolic functions from single-cell and spatial transcriptomics. Efficient and user-friendly, it runs on Python and integrates with Scanpy, enabling single-cell and spatial analysis of metabolic tasks.
systems-biology metabolism single-cell metabolic-pathways spatial-transcriptomics single-cell-transcriptomics metabolic-modeling
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Jan 20, 2025 - 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
A basic network of human metabolism, including key enzymes, intermediates, and hormonal influences
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Jul 10, 2018 - Swift
🤝 Tool for generating KEGG pathways completeness heatmaps from eggNOG-mapper annotations
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Dec 26, 2024 - Python
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
reconciliation chemoinformatics metabolic-models metabolic-network metabolic-reconstruction biochemical-reactions metabolites metabolic-pathways metabolite-identification
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Mar 8, 2018
PathVisio plugin to find relevant metabolic reactions from Rhea
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Apr 25, 2018 - Java
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
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
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
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