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    50 repositories

    • Naive_Bayes

      Public
      A Naive Bayes classifier for metagenomic data.
      C++
      •5•2•0•0•Updated Sep 23, 2024Sep 23, 2024

    • Scorpio

      Public
      Scorpio: Advancing Embeddings for Superior Biological Sequence Analysis
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • Incremental-Protein-Search

      Public
      Python
      •2•1•0•0•Updated Aug 20, 2024Aug 20, 2024

    • MetaBERTa

      Public
      Python
      •0•1•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 Prescreening
      Python
      •
      Other
      •0•0•0•0•Updated May 5, 2024May 5, 2024

    • bio-course-materials

      Public
      Course materials for a bioinformatics course.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•5•0•0•Updated Jan 23, 2024Jan 23, 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
      •1•3•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•5•0•0•Updated Aug 22, 2021Aug 22, 2021

    • BioDS_NCBI-Biopython_Notebooks

      Public
      Notebooks to introduce biopython
      Jupyter Notebook
      •96•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 causes COVID-19.
      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

    • themetagenomics

      Public
      R
      •
      Other
      •4•23•20•0•Updated May 6, 2020May 6, 2020

    • qiime2_tutorial

      Public
      Shell
      •2•2•0•0•Updated May 4, 2020May 4, 2020

    • SSIL

      Public
      Information and related links about the semi-supervised incremental learning project
      0•0•0•0•Updated Apr 9, 2020Apr 9, 2020

    • Learning-ML-Microbiome-Analysis-in-R

      Public
      Various tutorials and code from classes taught and previous work.
      TeX
      •1•0•0•0•Updated Mar 2, 2020Mar 2, 2020

    • microbiome_embeddings

      Public
      Python
      •2•10•1•0•Updated Feb 21, 2020Feb 21, 2020

    • 16s_embeddings

      Public
      Python
      •0•2•0•0•Updated Feb 21, 2020Feb 21, 2020

    • exploring_thematic_structure

      Public
      R
      •0•2•0•0•Updated Oct 23, 2019Oct 23, 2019

    • inbc-supporting-information

      Public
      Supporting Information of "Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life"
      0•1•0•0•Updated Sep 4, 2019Sep 4, 2019

    • Comp_Metagenomics_resources

      Public
      Materials for Computational Metagenomics class developed for NSF TUES project
      Jupyter Notebook
      •
      Other
      •1•8•0•0•Updated Jun 24, 2019Jun 24, 2019