Repositories list

• lab-website-template

  Public template
  An easy-to-use, flexible website template for labs.

  templatewebsitelab

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •387•463•7•0•Updated Jul 30, 2025Jul 30, 2025

• greenelab.com

  Public
  The website source code for greenelab.com

  jekyllwebsitelab+ 1greenelab

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •25•1•1•0•Updated Jul 30, 2025Jul 30, 2025

• scrumlord

  Public
  Continuous administration of the Greene Lab's electronic scrum

  administrationcrontravis-ci+ 2scrumcontinuous

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •9•13•2•1•Updated Jul 29, 2025Jul 29, 2025

• lwt-poster

  Public
  Poster on Lab Website Template

  TypeScript

  •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

• deconvolution_sc_sn_comparison

  Public
  The following repository is a work in progress. The Aim is to deconvolve samples with SC and SN, comparing performance.

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jul 9, 2025Jul 9, 2025

• HGSOC_Adipocytes

  Public
  Deconvolution of bulk RNA-seq samples of HGSOC including adipocytes.

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jul 7, 2025Jul 7, 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

• lab-website-template-docs

  Public
  GitBook documentation for Lab Website Template

  2•3•2•0•Updated Apr 7, 2025Apr 7, 2025

• hgsc_rnaseq_cluster

  Public
  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•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•2•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

• ccc

  Public
  Jupyter Notebook

  •

  Other

  •9•23•2•0•Updated Jan 17, 2025Jan 17, 2025

• hclust

  Public
  Agglomerative hierarchical clustering in JavaScript

  packagenodemath+ 4clusteringhierarchical-clusteringagglomerative-clusteringjavascript

  JavaScript

  •

  MIT License

  •3•19•0•0•Updated Dec 17, 2024Dec 17, 2024

• buddi

  Public
  BuDDI model implementation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •5•3•0•0•Updated Dec 5, 2024Dec 5, 2024

• onboarding

  Public
  Onboarding materials for the Greene Lab

  greenelabonboardingguidelines+ 3upennlab-carpentrylab

  Creative Commons Zero v1.0 Universal

  •22•31•1•0•Updated Nov 22, 2024Nov 22, 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•2•9•0•Updated Oct 25, 2024Oct 25, 2024

• pancancer-evaluation

  Public
  Evaluating genome-wide prediction of driver mutations using pan-cancer data

  classifiermachine-learninggenome+ 4cancerpancanceranalysisgene-expression

  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•0•0•2•Updated Aug 12, 2024Aug 12, 2024

• buddi_atac

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Aug 7, 2024Aug 7, 2024

• phenoplier_manuscript

  Public
  PhenoPLIER manuscript

  manuscriptunsupervised-learningcomplex-traits+ 2manubotgene-modules

  TeX

  •

  Other

  •4•1•1•3•Updated Jul 29, 2024Jul 29, 2024

• BioBombe

  Public
  BioBombe: Sequentially compressed gene expression features enhances biological signatures

  gene-setscompressionnetwork+ 6tcgagene-expressionautoencoderhetnetmsigdbbiobombe

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •26•66•2•0•Updated Jul 1, 2024Jul 1, 2024

• adage-backend

  Public
  The backend for Adage web app

  machine-learningweb-servergenomics+ 1interpretation

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •2•2•9•4•Updated Jun 26, 2024Jun 26, 2024

• manubot-gpt-manuscript

  Public
  Manuscript describing software for the automated revision of manubot manuscripts.

  TeX

  •

  Other

  •4•17•2•2•Updated Jun 20, 2024Jun 20, 2024

• aml_cfdna_atac

  Public
  Using BuDDI to integrate cfDNA and ATAC data from AML samples to identify cell of origin

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Apr 24, 2024Apr 24, 2024

• word-lapse

  Public
  Explore how a word changes over time

  reactmachine-learningnatural-language-processing

  JavaScript

  •

  Other

  •4•6•2•0•Updated Apr 17, 2024Apr 17, 2024

• phenoplier

  Public
  PhenoPLIER

  toolsoftwareunsupervised-learning+ 3complex-traitstwasgene-modules

  Jupyter Notebook

  •

  Other

  •5•13•6•0•Updated Apr 8, 2024Apr 8, 2024

• nature_news_manuscript

  Public
  HTML

  •

  Other

  •2•0•0•0•Updated Mar 15, 2024Mar 15, 2024