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    94 repositories

    • cNFDrugScreening

      Public
      This repository manages the code to analyze the results of drug screens in cNF organoids together with omics measurements of the tumor data.
      HTML
      •
      BSD 2-Clause "Simplified" License
      •0•2•1•1•Updated Nov 24, 2025Nov 24, 2025

    • coderdata

      Public
      Dataset package for facile training and testing of machine learning/AI algorithms that predict drug response in cancer model systems.
      machine-learningdeep-learningcancerdrug-responsebenchmark-dataset
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •3•19•22•0•Updated Nov 24, 2025Nov 24, 2025

    • Snekmer

      Public
      Pipeline to apply encoded Kmer analysis to protein sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•16•30•4•Updated Nov 21, 2025Nov 21, 2025

    • srpAnalytics

      Public
      This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
      R
      •
      Other
      •1•7•9•0•Updated Nov 20, 2025Nov 20, 2025

    • amlMultidrugResistance

      Public
      Jupyter Notebook
      •0•3•1•0•Updated Nov 20, 2025Nov 20, 2025

    • panSEA

      Public
      Multi-omic Set Enrichment Analysis
      R
      •
      Other
      •0•1•0•1•Updated Nov 18, 2025Nov 18, 2025

    • spammR

      Public
      Spatial Analysis of Multiomics Measurement in R
      R
      •
      BSD 2-Clause "Simplified" License
      •0•7•9•0•Updated Nov 13, 2025Nov 13, 2025

    • MPNST_Chr8

      Public
      R
      •
      MIT License
      •0•1•1•0•Updated Nov 13, 2025Nov 13, 2025

    • bmdrc

      Public
      Python library for the calculation of benchmark dose response curves
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•3•0•0•Updated Oct 13, 2025Oct 13, 2025

    • AML_sorted_proteomics

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Oct 11, 2025Oct 11, 2025

    • Exp21_NRAS_ASO_treated_patients

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • PythonCyc

      Public
      Python
      •
      MIT License
      •4•0•0•0•Updated Mar 28, 2025Mar 28, 2025

    • amlresistancenetworks

      Public
      R
      •2•3•3•0•Updated Feb 4, 2025Feb 4, 2025

    • BoltzmannMFX

      Public
      BoltzmannMFX is a biological simulation code that solves chemical reaction networks using maximum entropy methods. It uses modules from MFiX-Exa and is based on the AMReX framework for massively parallel block-structured adaptive mesh applications.
      C++
      •
      BSD 2-Clause "Simplified" License
      •2•2•6•2•Updated Nov 28, 2024Nov 28, 2024

    • cdrp

      Public
      Python
      •0•1•0•1•Updated Sep 16, 2024Sep 16, 2024

    • CLEAN-Contact

      Public
      PyTorch Implementation of CLEAN-Contact: Contrastive Learning-enabled Enzyme Functional Annotation Prediction with Structural Inference
      deep-learningpytorchenzyme-functioncontrastive-learningai4science
      Python
      •
      Other
      •4•11•0•0•Updated May 29, 2024May 29, 2024

    • SElon7942-GEM

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated May 24, 2024May 24, 2024

    • SERGIO

      Public
      A simulator for single-cell expression data guided by gene regulatory networks
      HTML
      •
      GNU General Public License v3.0
      •31•0•9•2•Updated May 8, 2024May 8, 2024

    • ProchlorococcusGEM

      Public
      Python
      •0•1•0•0•Updated Mar 30, 2024Mar 30, 2024

    • cNFOrganoidAnalysis

      Public
      R
      •1•4•4•0•Updated Mar 11, 2024Mar 11, 2024

    • BeatAMLproteomics

      Public
      Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC
      HTML
      •
      MIT License
      •3•9•8•1•Updated Mar 5, 2024Mar 5, 2024

    • ML_UVvisModels

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •2•14•1•0•Updated Feb 20, 2024Feb 20, 2024

    • Exp22_CRISPR-Cas9_NRAS_KO_cell_lines

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 16, 2024Feb 16, 2024

    • emll

      Public
      some code for linlog model simulation
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •4•3•4•2•Updated Jan 18, 2024Jan 18, 2024

    • decomprolute

      Public
      A suite of scientific workflows to assess metrics to compare efficacy of protein-based tumor deconvolution algorithms.
      Common Workflow Language
      •
      MIT License
      •5•16•4•0•Updated Jan 15, 2024Jan 15, 2024

    • EinsumNetworks

      Public
      Python
      •21•1•0•0•Updated Jan 14, 2024Jan 14, 2024

    • AdvancedProbabilisticCircuits.jl

      Public
      Probabilistic Circuits in Julia
      Julia
      •
      MIT License
      •2•0•0•0•Updated Dec 27, 2023Dec 27, 2023

    • CONCERTO

      Public
      Continuous integration and validation for genome-scale metabolic model consortia
      HTML
      •
      Apache License 2.0
      •3•3•52•0•Updated Dec 5, 2023Dec 5, 2023

    • panCancerModelSystems

      Public
      This project will explore the differences between model systems to identify systemic biases across tumors and models toward mapping from one to the other.
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •0•3•0•0•Updated Dec 4, 2023Dec 4, 2023

    • CLEAN_ESM2

      Public
      CLEAN: a contrastive learning model for high-quality functional prediction of proteins (using ESM2)
      Python
      •
      MIT License
      •59•0•0•0•Updated Nov 29, 2023Nov 29, 2023