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    41 repositories

    • MGM

      Public
      MGM (Microbial General Model) as a large-scaled pretrained language model for interpretable microbiome data analysis.
      Python
      •
      MIT License
      •0•16•0•0•Updated Feb 17, 2025Feb 17, 2025

    • DeepMicroFinder

      Public
      0•0•0•0•Updated Feb 11, 2025Feb 11, 2025

    • Moutai-Catalog

      Public
      R
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • ASD-cancer

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 16, 2024Oct 16, 2024

    • DeepInverton

      Public
      Python
      •
      MIT License
      •1•1•0•0•Updated Sep 3, 2024Sep 3, 2024

    • BGC-Prophet

      Public
      Python
      •
      MIT License
      •0•4•0•0•Updated Mar 26, 2024Mar 26, 2024

    • ONN4ARG

      Public
      ONN4ARG is an ontology-aware neural network model, which employs a novel ontology-aware layer for antibiotic resistance gene prediction and classification.
      Python
      •
      GNU General Public License v3.0
      •1•2•2•0•Updated Jan 6, 2024Jan 6, 2024

    • Moutai-SME

      Public
      The codes, mathematical equations and data sources involved in Moutai-SME project.
      0•0•0•0•Updated Jan 3, 2024Jan 3, 2024

    • Skin_paper_codes

      Public
      R
      •0•0•0•0•Updated Nov 21, 2023Nov 21, 2023

    • DeepTaxa

      Public
      DeepTaxa: a deep learning approach for ultra-fast classification of genomes
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Sep 28, 2023Sep 28, 2023

    • DeepMicroCancer

      Public
      Python
      •0•3•0•0•Updated Apr 6, 2023Apr 6, 2023

    • Meta-Sorter

      Public
      Improving biome labeling for tens of thousands of inaccurately annotated microbial community samples based on neural network and transfer learning
      Shell
      •0•1•0•0•Updated Mar 25, 2023Mar 25, 2023

    • biome-species-function-relationship

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 17, 2023Feb 17, 2023

    • microDELTA

      Public
      PureBasic
      •0•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • SAM

      Public
      SAM (skin age model) is used to assess the skin state from the phenotypic and microbial perspectives.
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 14, 2022Nov 14, 2022

    • ONN4MST

      Public
      Ontology-aware neural network (ONN) for microbial community sample source tracking!
      neural-networkontology-searchmicrobiome-model
      Python
      •
      GNU General Public License v3.0
      •1•11•1•1•Updated Oct 11, 2022Oct 11, 2022

    • GAN-GMHI

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•2•1•0•Updated Oct 5, 2022Oct 5, 2022

    • EXPERT

      Public
      Transfer Learning-enabled context-aware microbial source tracking
      deep-learningmicrobial-source-trackingtransfer-learning
      Python
      •
      MIT License
      •4•13•3•0•Updated Oct 4, 2022Oct 4, 2022

    • EXPERT-Disease-GGMP

      Public
      Overcoming regional limitations: Transfer learning for cross-regional microbial-based diagnosis of diseases
      R
      •1•8•1•0•Updated Sep 6, 2022Sep 6, 2022

    • Meta-Prism-2.0

      Public
      Efficient microbial communities similarites calculation and comparison tool
      C++
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Apr 26, 2022Apr 26, 2022

    • MetaSource

      Public
      The source code and intermediate results of "Structure and function predictions of protein families by a microbiome-based targeted approach: decoding the link of microbiome niches with protein family homologous sequences"
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Sep 4, 2021Sep 4, 2021

    • EXPERT-use-cases

      Public
      Reproducible research, and functional show-cases for EXPERT.
      deep-learningtransfer-learningmicrobiomedisease-modelingexpert
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 28, 2021May 28, 2021

    • TAT-dataset

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • COVID-19-CAM

      Public
      Cohort Adaptive Model: CAM for COVID-19
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 4, 2020Oct 4, 2020

    • Biome-sorter

      Public
      Biome-sorter: an Ontology-aware Neural Network enhanced auto sorter for microbial community sample without biome source information.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Sep 27, 2020Sep 27, 2020

    • HPC-Manual

      Public
      This repo is created for a full explanation about how HPC servers are deployed and configured by administrators, also used as user manual for lab members.
      0•0•0•0•Updated Jun 28, 2020Jun 28, 2020

    • Correlation-Centric-Network

      Public
      Source code for the research:"Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology "
      C++
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated May 29, 2020May 29, 2020

    • metaPrism

      Public
      Ultra-fast and highly accurate microbial community structure search utilizing dual-indexing and parallel computation
      metagenomic-samples-analysis
      C++
      •
      GNU General Public License v3.0
      •1•5•0•0•Updated May 5, 2020May 5, 2020

    • DLMER-Bio

      Public
      R
      •0•0•0•0•Updated Dec 20, 2019Dec 20, 2019

    • straingems

      Public
      straingems
      Python
      •1•3•1•0•Updated Mar 28, 2019Mar 28, 2019