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    91 repositories

    • 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•17•35•2•Updated Aug 6, 2025Aug 6, 2025

    • AML_sorted_proteomics

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • Snekmer

      Public
      Pipeline to apply encoded Kmer analysis to protein sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•16•27•4•Updated Jul 30, 2025Jul 30, 2025

    • MPNST_Chr8

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • spammR

      Public
      Spatial Analysis of Multiomics Measurement in R
      R
      •
      BSD 2-Clause "Simplified" License
      •0•5•6•0•Updated Jul 25, 2025Jul 25, 2025

    • bmdrc

      Public
      Python library for the calculation of benchmark dose response curves
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•2•0•0•Updated Jun 11, 2025Jun 11, 2025

    • panSEA

      Public
      Multi-omic Set Enrichment Analysis
      R
      •
      MIT License
      •0•0•0•0•Updated May 1, 2025May 1, 2025

    • 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.
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•0•1•0•Updated Apr 25, 2025Apr 25, 2025

    • PythonCyc

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

    • srpAnalytics

      Public
      This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
      R
      •
      Other
      •1•6•5•0•Updated Feb 20, 2025Feb 20, 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•1•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
      •30•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
      •1•13•1•0•Updated Feb 20, 2024Feb 20, 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
      •57•0•0•0•Updated Nov 29, 2023Nov 29, 2023

    • HomeownershipDisparity_2015_2019

      Public
      Code associated with work presented in Race-Specific Risk Factors for Homeownership Disparity in the Continental United States
      HTML
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2023Nov 10, 2023

    • proteomics-drug-response

      Public
      This repository will serve as the primary base to develop tools to assess and predict drug response from proteomics measurements in cancer model systems.
      0•1•0•0•Updated Oct 9, 2023Oct 9, 2023

    • spatial-proteomics-mapping

      Public
      Here we are evaluating the ability to measure spatially resolved proteomics
      R
      •0•0•2•0•Updated Sep 8, 2023Sep 8, 2023