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biocyc

Here are 8 public repositories matching this topic...

hallamlab / pathway2vec

Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction

bioinformatics deep-learning metapath embedding pathway-prediction metacyc heterogeneous-information-networks biocyc pathway-tools

Updated Jul 8, 2021
Python

hallamlab / mlLGPR

Metabolic pathway inference using multi-label classification with rich pathway features

bioinformatics metagenomics logistic-regression multi-label-learning pathway-prediction metacyc biocyc pathway-tools

Updated Jul 6, 2023
Python

ouzounis / MjCyc

MjCyc Tier 2 PGDB at BioCyc

genome-annotation pathway-analysis genome-analysis archaea biocyc

Updated Jan 25, 2025

hallamlab / reMap

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

Updated Nov 8, 2021
Python

arbasher / prepBioCyc

prepBioCyc: Preprocess BioCyc files

bioinformatics graph metagenomics bioinformatics-pipeline heterogeneous-network data-wrangling bioinformatics-analysis metabolic-network metacyc metabolic-pathways bioinformatics-tool biocyc

Updated Apr 27, 2022
Python

hallamlab / triUMPF

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

Updated Sep 19, 2021
Python

hallamlab / chap

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

Updated Nov 8, 2021
Python

hallamlab / leADS

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

Updated Nov 16, 2021
Python

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