Repositories list

• BGC-Finder

  Public
  Jupyter Notebook

  •2•1•0•0•Updated Jul 8, 2025Jul 8, 2025

• BGC-Prophet

  Public
  A deep learning approach that leverages language processing neural network model to accurately identify known BGCs and extrapolate novel ones.

  Python

  •

  MIT License

  •0•14•0•0•Updated May 28, 2025May 28, 2025

• MGM

  Public
  MGM (Microbial General Model) as a large-scaled pretrained language model for interpretable microbiome data analysis.

  deep-learningmicrobiome-modelfoundation-models-for-biology

  Jupyter Notebook

  •

  MIT License

  •0•30•0•0•Updated Apr 17, 2025Apr 17, 2025

• DeepMicroFinder

  Public
  R

  •0•2•0•0•Updated Apr 16, 2025Apr 16, 2025

• MicroProphet

  Public
  MicroProphet is a transformer-based digital twin model for microbial time-series prediction, designed to accurately forecast microbial dynamics without requiring data alignment or imputation, making it suitable for diverse and irregular microbiome datasets.

  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 14, 2025Apr 14, 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

• 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•4•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•12•1•1•Updated Oct 11, 2022Oct 11, 2022

• GAN-GMHI

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •3•2•0•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•14•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-learningmicrobiome+ 2disease-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