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    59 repositories

    • dna-ssl-augmentations

      Public
      Python
      •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • glm-epinet-pyt

      Public
      Pytorch implementation of Epinet, along with usage for genomic language models
      Python
      •1•0•0•0•Updated Mar 13, 2026Mar 13, 2026

    • MicroTraitLLM

      Public
      A retrieval-augmented generation (RAG) LLM which utilizes zero-shot and single-shot prompting to give specific, citation-based answers for researchers.
      Python
      •2•0•0•1•Updated Mar 9, 2026Mar 9, 2026

    • Naive_Bayes

      Public
      A Naive Bayes classifier for metagenomic data.
      C++
      •5•2•0•0•Updated Feb 6, 2026Feb 6, 2026

    • NBC-novelty-detection

      Public
      NBC++ novelty detection repo
      Python
      •
      MIT License
      •1•0•0•0•Updated Jan 31, 2026Jan 31, 2026

    • nevermore

      Public
      Python
      •
      Other
      •1•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • carmania

      Public
      Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis [NeurIPS2025]
      Jupyter Notebook
      •
      MIT License
      •1•6•0•0•Updated Nov 18, 2025Nov 18, 2025

    • bio-course-materials

      Public
      Course materials for a bioinformatics course.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •5•4•0•1•Updated Nov 5, 2025Nov 5, 2025

    • Firm-DTI

      Public
      Python
      •
      Apache License 2.0
      •1•1•0•0•Updated Oct 20, 2025Oct 20, 2025

    • genomics-ncd-gzip

      Public
      Project to utilize gzip and ncd for genomics data processing
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • Genomics-Language-Model-Comparison

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 20, 2025Jun 20, 2025

    • Scorpio

      Public
      Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization
      Python
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Apr 1, 2025Apr 1, 2025

    • Incremental-Protein-Search

      Public
      Python
      •2•1•0•0•Updated Feb 18, 2025Feb 18, 2025

    • MetaBERTa

      Public
      Python
      •1•3•0•0•Updated Jun 30, 2024Jun 30, 2024

    • FDSL_Evo

      Public
      Repository for code from Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreenin…
      Python
      •
      Other
      •0•2•0•0•Updated May 5, 2024May 5, 2024

    • Complet-Plus

      Public
      Complet-Plus by Rachel Nguyen and Drexel EESI Lab
      Shell
      •2•3•0•0•Updated Mar 30, 2023Mar 30, 2023

    • covid_severity

      Public
      Predicting COVID-19 Disease Severity from Spike Genotype Based on Global Sequencing Data
      Python
      •1•0•0•0•Updated May 26, 2022May 26, 2022

    • Covid

      Public
      SARS-CoV-2 Spike Sequence Variant Analysis Using Interpretable Deep Learning
      Jupyter Notebook
      •2•0•0•0•Updated May 26, 2022May 26, 2022

    • PTAB

      Public
      Analysis and Outcome Prediction for USPTO Patent Trial and Appeals Board proceedings and decisions.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Mar 30, 2022Mar 30, 2022

    • MetaMutationalSigs

      Public
      https://hub.docker.com/r/pp535/metamutationalsigs
      HTML
      •2•4•0•0•Updated Dec 8, 2021Dec 8, 2021

    • TEA

      Public
      (Taxa Evaluation and Assessment) Parse, organize, calculate and save data from metagenomic profile files
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Nov 5, 2021Nov 5, 2021

    • seq2att

      Public
      Python
      •2•3•0•0•Updated Oct 3, 2021Oct 3, 2021

    • sequence_attention

      Public
      Learning, Visualizing and Exploring 16S rRNA Structure Using an Attention-based Deep Neural Network
      Jupyter Notebook
      •3•6•0•0•Updated Aug 22, 2021Aug 22, 2021

    • BioDS_NCBI-Biopython_Notebooks

      Public
      Notebooks to introduce biopython
      Jupyter Notebook
      •100•3•0•0•Updated Jul 21, 2021Jul 21, 2021

    • bio-course-project

      Public
      2•0•0•0•Updated Mar 25, 2021Mar 25, 2021

    • intro-to-picotte

      Public
      Shell
      •1•0•0•0•Updated Mar 18, 2021Mar 18, 2021

    • ncov_ism

      Public
      Informative Subtype Marker (ISM) is an efficient framework for genetic subtyping of a pandemic virus and implement it for SARS-CoV-2, the novel coronavirus that…
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Mar 5, 2021Mar 5, 2021

    • fastddtw

      Public
      Jupyter Notebook
      •8•0•0•0•Updated Dec 15, 2020Dec 15, 2020

    • AttentionGO

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Nov 25, 2020Nov 25, 2020

    • ISM

      Public
      Jupyter Notebook
      •
      Other
      •4•9•0•0•Updated Aug 25, 2020Aug 25, 2020
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