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    • scrumlord

      Public
      Continuous administration of the Greene Lab's electronic scrum
      Python
      BSD 3-Clause "New" or "Revised" License
      101320Updated Apr 22, 2026Apr 22, 2026
    • greenelab.com

      Public
      The website source code for greenelab.com
      HTML
      BSD 3-Clause "New" or "Revised" License
      26310Updated Apr 13, 2026Apr 13, 2026
    • This repository contains scripts testing aggregate degree weighted path count (DWPC) statistics.
      Python
      BSD 3-Clause "New" or "Revised" License
      1100Updated Apr 9, 2026Apr 9, 2026
    • ccc

      Public
      Jupyter Notebook
      Other
      92421Updated Mar 4, 2026Mar 4, 2026
    • Analysis of GitHub repository and project content.
      Python
      BSD 3-Clause "New" or "Revised" License
      1000Updated Feb 27, 2026Feb 27, 2026
    • Onboarding materials for the Greene Lab
      Creative Commons Zero v1.0 Universal
      243311Updated Feb 10, 2026Feb 10, 2026
    • Deconvolution of bulk RNA-seq samples of HGSOC including adipocytes.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      1000Updated Jan 26, 2026Jan 26, 2026
    • deconvolution_sc_sn_comparison

      Public
      This repository contains all code for the work done in the research paper titled "Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deco…
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      1000Updated Jan 6, 2026Jan 6, 2026
    • lab-website-template

      Public template
      An easy-to-use, flexible website template for labs. https://doi.org/10.5281/zenodo.17228741
      HTML
      BSD 3-Clause "New" or "Revised" License
      43654670Updated Nov 17, 2025Nov 17, 2025
    • lwt-poster

      Public
      Poster on Lab Website Template
      TypeScript
      0100Updated Sep 30, 2025Sep 30, 2025
    • Algorithm development for context aware path search through biomedical knowledge graphs.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      2000Updated Sep 25, 2025Sep 25, 2025
    • GitBook documentation for Lab Website Template
      1320Updated Sep 24, 2025Sep 24, 2025
    • dwpc_rnn

      Public
      Testing RNNs for creating degree-weighted pathway null distributions
      BSD 3-Clause "New" or "Revised" License
      1000Updated Aug 19, 2025Aug 19, 2025
    • The following repository is a work in progress. the Aim is to deconvolve HGSOC samples with added adipocyte signal.
      R
      BSD 3-Clause "New" or "Revised" License
      2001Updated Jun 16, 2025Jun 16, 2025
    • HTML
      BSD 3-Clause "New" or "Revised" License
      0110Updated Mar 27, 2025Mar 27, 2025
    • Predicting missing cell-type proportions from deconvolution residual using NNLS.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      1300Updated Mar 12, 2025Mar 12, 2025
    • Ongoing project on deconvolution using higher-dimensional image representations of gene expression data.
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      1000Updated Mar 10, 2025Mar 10, 2025
    • backup

      Public
      Backup a GitHub user's or organization's repos and wikis
      TypeScript
      0000Updated Jan 31, 2025Jan 31, 2025
    • hclust

      Public
      Agglomerative hierarchical clustering in JavaScript
      JavaScript
      MIT License
      21900Updated Dec 17, 2024Dec 17, 2024
    • buddi

      Public
      BuDDI model implementation
      Python
      BSD 3-Clause "New" or "Revised" License
      5400Updated Dec 5, 2024Dec 5, 2024
    • HTML
      Creative Commons Attribution 4.0 International
      1000Updated Nov 11, 2024Nov 11, 2024
    • Analysis notebooks for the BuDDI manuscript
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      3390Updated Oct 25, 2024Oct 25, 2024
    • Evaluating genome-wide prediction of driver mutations using pan-cancer data
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      18170Updated Oct 21, 2024Oct 21, 2024
    • HTML
      Other
      2103Updated Sep 6, 2024Sep 6, 2024
    • Implementation of a VAE in scvi-tools for single-cell and single-nucleus translation.
      Python
      BSD 3-Clause "New" or "Revised" License
      2102Updated Aug 12, 2024Aug 12, 2024
    • Jupyter Notebook
      1000Updated Aug 7, 2024Aug 7, 2024
    • PhenoPLIER manuscript
      TeX
      Other
      4113Updated Jul 29, 2024Jul 29, 2024
    • BioBombe

      Public
      BioBombe: Sequentially compressed gene expression features enhances biological signatures
      Jupyter Notebook
      BSD 3-Clause "New" or "Revised" License
      266520Updated Jul 1, 2024Jul 1, 2024
    • The backend for Adage web app
      Python
      BSD 3-Clause "New" or "Revised" License
      2294Updated Jun 26, 2024Jun 26, 2024
    • Manuscript describing software for the automated revision of manubot manuscripts.
      TeX
      Other
      41622Updated Jun 20, 2024Jun 20, 2024
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