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    179 repositories

    • scrumlord

      Public
      Continuous administration of the Greene Lab's electronic scrum
      administrationcrontravis-ci
      administrationcrontravis-ciscrumcontinuous
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•13•2•0•Updated Jun 24, 2026Jun 24, 2026

    • fm-pm-eval-manuscript

      Public
      Collaborative manuscript for companion repo: github.com/greenelab/fm-pm-evaluator.
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•1•Updated Jun 20, 2026Jun 20, 2026

    • multi-dwpc

      Public
      This repository contains scripts testing aggregate degree weighted path count (DWPC) statistics.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jun 16, 2026Jun 16, 2026

    • fm-pm-evaluator

      Public
      Realizing the benefits of foundation models requires careful evaluations that map the boundaries of generalization.
      Python
      •
      BSD 2-Clause "Simplified" License
      •1•0•0•0•Updated Jun 16, 2026Jun 16, 2026

    • lab-website-template

      Public template
      An easy-to-use, flexible website template for labs. https://doi.org/10.5281/zenodo.17228741
      templatewebsitelab
      templatewebsitelab
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •441•557•7•0•Updated Jun 2, 2026Jun 2, 2026

    • miQC

      Public
      Flexible, probablistic metrics for quality control of scRNA-seq data
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•22•2•2•Updated May 27, 2026May 27, 2026

    • T21-eQTL

      Public
      Cohort-scale extension of Hunter et al. (2023) "Transcription dosage compensation does not occur in Down syndrome" (BMC Biology 21:228), applied to the Human Tr…
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated May 15, 2026May 15, 2026

    • onboarding

      Public
      Onboarding materials for the Greene Lab
      labgreenelabonboarding
      labgreenelabonboardingguidelinesupennlab-carpentry
      Creative Commons Zero v1.0 Universal
      •24•33•1•0•Updated May 12, 2026May 12, 2026

    • repository_analysis

      Public
      Analysis of GitHub repository and project content.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Apr 28, 2026Apr 28, 2026

    • greenelab.com

      Public
      The website source code for greenelab.com
      jekyllwebsitelab
      jekyllwebsitelabgreenelab
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •26•3•1•0•Updated Apr 13, 2026Apr 13, 2026

    • ccc

      Public
      Jupyter Notebook
      •
      Other
      •9•24•2•1•Updated Mar 4, 2026Mar 4, 2026

    • HGSOC_Adipocytes

      Public
      Deconvolution of bulk RNA-seq samples of HGSOC including adipocytes.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated 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
      •1•0•0•0•Updated Jan 6, 2026Jan 6, 2026

    • lwt-poster

      Public
      Poster on Lab Website Template
      TypeScript
      •0•1•0•0•Updated Sep 30, 2025Sep 30, 2025

    • Context-Aware-Path-Probability

      Public
      Algorithm development for context aware path search through biomedical knowledge graphs.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • lab-website-template-docs

      Public
      GitBook documentation for Lab Website Template
      1•3•2•0•Updated Sep 24, 2025Sep 24, 2025

    • dwpc_rnn

      Public
      Testing RNNs for creating degree-weighted pathway null distributions
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Aug 19, 2025Aug 19, 2025

    • deconvolution_adipocytes

      Public
      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
      •2•0•0•1•Updated Jun 16, 2025Jun 16, 2025

    • hgsc_rnaseq_cluster

      Public
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•1•0•Updated Mar 27, 2025Mar 27, 2025

    • pred_missing_celltypes

      Public
      Predicting missing cell-type proportions from deconvolution residual using NNLS.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•3•0•0•Updated Mar 12, 2025Mar 12, 2025

    • CNN_deconvolution

      Public
      Ongoing project on deconvolution using higher-dimensional image representations of gene expression data.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Mar 10, 2025Mar 10, 2025

    • backup

      Public
      Backup a GitHub user's or organization's repos and wikis
      TypeScript
      •0•0•0•0•Updated Jan 31, 2025Jan 31, 2025

    • hclust

      Public
      Agglomerative hierarchical clustering in JavaScript
      javascriptpackagenode
      javascriptpackagenodemathclusteringhierarchical-clusteringagglomerative-clustering
      JavaScript
      •
      MIT License
      •2•19•0•0•Updated Dec 17, 2024Dec 17, 2024

    • buddi

      Public
      BuDDI model implementation
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•0•0•Updated Dec 5, 2024Dec 5, 2024

    • generalization-manuscript

      Public
      HTML
      •
      Creative Commons Attribution 4.0 International
      •1•0•0•0•Updated Nov 11, 2024Nov 11, 2024

    • buddi_analysis

      Public
      Analysis notebooks for the BuDDI manuscript
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•9•0•Updated Oct 25, 2024Oct 25, 2024

    • pancancer-evaluation

      Public
      Evaluating genome-wide prediction of driver mutations using pan-cancer data
      classifiermachine-learninggenome
      classifiermachine-learninggenomeanalysiscancergene-expressionpancancer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•17•0•Updated Oct 21, 2024Oct 21, 2024

    • ccc-manuscript

      Public
      HTML
      •
      Other
      •2•1•0•3•Updated Sep 6, 2024Sep 6, 2024

    • single_translator_VAE

      Public
      Implementation of a VAE in scvi-tools for single-cell and single-nucleus translation.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•0•2•Updated Aug 12, 2024Aug 12, 2024

    • buddi_atac

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Aug 7, 2024Aug 7, 2024
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