Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
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Updated
May 8, 2024 - Python
Toolkit for Modelling and Simulation of Gene Expressions and Metabolism
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
Infer metabolic directions from moment differences of mass-weighted intensity distributions
A tool for representing genomic potential and transcriptomic expression into KEGG pathways
Go REST API to replace Genbank, Uniprot, Rhea, and CHEMBL
Diversity-based enumeration of optimal context-specific metabolic networks
leADS: improved metabolic pathway inference based on active dataset subsampling
Metabolic pathway inference using non-negative matrix factorization with community detection
CHAP: Modeling Metabolic Pathways as Groups (with Augmentation)
Pipeline plugins for PALADIN, providing HPC support, abundance (taxonomy, go terms), customized reports, etc
PathVisio plugin to find relevant metabolic reactions from Rhea
prepBioCyc: Preprocess BioCyc files
Serves as the backend code for https://www.curatemetabolicpathways.com
streamlit application for metabolic json from BIGG modelling database.
a slint interface to the BIGG modeler database establishing all the links to the metanextx
MNXref: Reconciliation of metabolites and biochemical reactions for metabolic networks
scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.
reMap: relabeling metabolic pathway data with groups to improve prediction outcomes
Web application of metabolics pathway visualisation, for the Gencovery business (https://gencovery.com/), created during the PDP project during the M1 of the Master of Bioinformatics, in Bordeaux.
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