Greene Laboratory

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171 repositories

pred_missing_celltypes
Public
Predicting missing cell-type proportions from deconvolution residual using NNLS.
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•2•0•0•Updated Feb 8, 2025Feb 8, 2025
scrumlord
Public
Continuous administration of the Greene Lab's electronic scrum
administration cron travis-ci scrum continuous
Python
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BSD 3-Clause "New" or "Revised" License
•8•13•2•0•Updated Feb 7, 2025Feb 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
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BSD 3-Clause "New" or "Revised" License
•2•0•0•1•Updated Feb 4, 2025Feb 4, 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.
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Feb 3, 2025Feb 3, 2025
lab-website-template
Public template
An easy-to-use, flexible website template for labs.
template website lab
HTML
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BSD 3-Clause "New" or "Revised" License
•326•385•6•0•Updated Feb 3, 2025Feb 3, 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
greenelab.com
Public
The website source code for greenelab.com
jekyll website lab greenelab
HTML
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BSD 3-Clause "New" or "Revised" License
•25•1•2•0•Updated Jan 30, 2025Jan 30, 2025
lab-website-template-docs
Public
GitBook documentation for Lab Website Template
2•1•2•0•Updated Jan 27, 2025Jan 27, 2025
ccc
Public
Jupyter Notebook
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Other
•8•23•2•0•Updated Jan 17, 2025Jan 17, 2025
hclust
Public
Agglomerative hierarchical clustering in JavaScript
package node math clustering hierarchical-clustering agglomerative-clustering javascript
JavaScript
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MIT License
•3•18•0•0•Updated Dec 17, 2024Dec 17, 2024
buddi
Public
BuDDI model implementation
Python
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BSD 3-Clause "New" or "Revised" License
•3•2•0•0•Updated Dec 5, 2024Dec 5, 2024
onboarding
Public
Onboarding materials for the Greene Lab
greenelab onboarding guidelines upenn lab-carpentry lab
Creative Commons Zero v1.0 Universal
•22•31•1•0•Updated Nov 22, 2024Nov 22, 2024
generalization-manuscript
Public
HTML
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Creative Commons Attribution 4.0 International
•1•0•0•0•Updated Nov 11, 2024Nov 11, 2024
CNN_deconvolution
Public
Ongoing project on deconvolution using higher-dimensional image representations of gene expression data.
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Oct 30, 2024Oct 30, 2024
buddi_analysis
Public
Analysis notebooks for the BuDDI manuscript
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•2•2•9•0•Updated Oct 25, 2024Oct 25, 2024
pancancer-evaluation
Public
Evaluating genome-wide prediction of driver mutations using pan-cancer data
classifier machine-learning genome cancer pancancer analysis gene-expression
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•1•9•17•0•Updated Oct 21, 2024Oct 21, 2024
ccc-manuscript
Public
HTML
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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
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BSD 3-Clause "New" or "Revised" License
•1•0•0•1•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
manuscript unsupervised-learning complex-traits manubot gene-modules
TeX
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Other
•4•1•1•3•Updated Jul 29, 2024Jul 29, 2024
BioBombe
Public
BioBombe: Sequentially compressed gene expression features enhances biological signatures
gene-sets compression network tcga gene-expression autoencoder hetnet msigdb biobombe
Jupyter Notebook
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BSD 3-Clause "New" or "Revised" License
•25•65•2•0•Updated Jul 1, 2024Jul 1, 2024
adage-backend
Public
The backend for Adage web app
machine-learning web-server genomics interpretation
Python
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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
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Other
•3•17•2•2•Updated Jun 20, 2024Jun 20, 2024
hgsc_rnaseq_cluster
Public
HTML
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BSD 3-Clause "New" or "Revised" License
•0•0•1•0•Updated Jun 7, 2024Jun 7, 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
react machine-learning natural-language-processing
JavaScript
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Other
•4•6•2•0•Updated Apr 17, 2024Apr 17, 2024
phenoplier
Public
PhenoPLIER
tool software unsupervised-learning complex-traits twas gene-modules
Jupyter Notebook
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Other
•5•12•6•0•Updated Apr 8, 2024Apr 8, 2024
nature_news_manuscript
Public
HTML
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Other
•2•0•0•0•Updated Mar 15, 2024Mar 15, 2024
nature_news_disparities
Public
Analysis pipeline for Nature news articles
analysis
R
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BSD 3-Clause "New" or "Revised" License
•1•5•5•0•Updated Feb 12, 2024Feb 12, 2024
xswap-manuscript
Public
Manuscript on XSwap network permutation and hetnet node degrees
networks permutation hetnets xswap manuscript manubot
HTML
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Other
•5•3•0•0•Updated Feb 10, 2024Feb 10, 2024