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@PNNL-CompBio Computational Biology @Pacific Northwest National Laboratory

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    97 repositories

    • amlMultidrugResistance

      Public
      Jupyter Notebook
      •0•3•0•1•Updated Sep 3, 2026Sep 3, 2026

    • spammR

      Public
      Spatial Analysis of Multiomics Measurement in R
      spatialproteomicsmetabolomics
      spatialproteomicsmetabolomicslipidomics
      R
      •
      BSD 2-Clause "Simplified" License
      •1•7•7•0•Updated Sep 3, 2026Sep 3, 2026

    • srpAnalytics

      Public
      This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
      Python
      •
      Other
      •1•7•10•0•Updated Sep 3, 2026Sep 3, 2026

    • bmdrc

      Public
      Python library for the calculation of benchmark dose response curves
      HTML
      •
      BSD 2-Clause "Simplified" License
      •2•3•0•0•Updated Sep 3, 2026Sep 3, 2026

    • MPNST-PDX-MT

      Public
      Here we have our analysis and modeling of drug response in MPNST PDX-MT samples
      R
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Aug 26, 2026Aug 26, 2026

    • smairt-template

      Public
      The Scientific Method using AI Research Template for cookiecutter
      Python
      •3•4•1•1•Updated Aug 24, 2026Aug 24, 2026

    • coderdata

      Public
      Dataset package for facile training and testing of machine learning/AI algorithms that predict drug response in cancer model systems.
      machine-learningdeep-learningcancer
      machine-learningdeep-learningcancerdrug-responsebenchmark-dataset
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •4•21•31•1•Updated Aug 13, 2026Aug 13, 2026

    • lipid_pathway_integrator

      Public
      Unifies lipid ontology-aware representation and pathway-based multi-omics integration in a single framework
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•0•0•Updated Aug 12, 2026Aug 12, 2026

    • HomeownershipDisparity_2015_2019

      Public archive
      Code associated with work presented in Race-Specific Risk Factors for Homeownership Disparity in the Continental United States
      HTML
      •
      MIT License
      •0•0•1•0•Updated Jul 20, 2026Jul 20, 2026

    • NEATO

      Public archive
      R
      •0•1•5•0•Updated Jul 20, 2026Jul 20, 2026

    • decomprolute

      Public archive
      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 Jul 6, 2026Jul 6, 2026

    • p3

      Public archive
      The PNNL Proteomics Pipeline - fork to do your own analysis.
      R
      •
      MIT License
      •1•3•1•0•Updated Jul 6, 2026Jul 6, 2026

    • cNFOrganoidAnalysis

      Public archive
      R
      •1•4•4•0•Updated Jul 6, 2026Jul 6, 2026

    • cytokineDrugResistance

      Public archive
      Studying the impacts of cytokines on drug resistance in AML
      HTML
      •
      MIT License
      •2•1•2•0•Updated Jul 6, 2026Jul 6, 2026

    • beatAMLpilotProteomics

      Public archive
      Analysis of BEAT AML patient proteomics data
      R
      •
      MIT License
      •2•1•0•1•Updated Jul 6, 2026Jul 6, 2026

    • earlyLateAMLresistance

      Public archive
      Investigations into differences between early and late resistance in AML patients
      R
      •
      MIT License
      •2•1•2•0•Updated Jul 6, 2026Jul 6, 2026

    • Snekmer

      Public
      Pipeline to apply encoded Kmer analysis to protein sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•17•30•3•Updated Jun 22, 2026Jun 22, 2026

    • 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•0•Updated Apr 14, 2026Apr 14, 2026

    • ion-mob-ms

      Public
      Workflow for analyzing ion mobility ms-ms data
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•3•10•0•Updated Mar 6, 2026Mar 6, 2026

    • MPNST_Chr8

      Public
      R
      •
      MIT License
      •0•1•1•0•Updated Feb 10, 2026Feb 10, 2026

    • panSEA

      Public
      Multi-omic Set Enrichment Analysis
      R
      •
      Other
      •0•1•1•1•Updated Dec 23, 2025Dec 23, 2025

    • PythonCyc

      Public
      Python
      •
      MIT License
      •4•0•0•0•Updated Dec 3, 2025Dec 3, 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•1•0•Updated Sep 25, 2025Sep 25, 2025

    • amlresistancenetworks

      Public
      R
      •2•3•4•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 o…
      C++
      •
      BSD 2-Clause "Simplified" License
      •4•2•6•2•Updated Nov 28, 2024Nov 28, 2024

    • cdrp

      Public
      Python
      •0•1•1•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-function
      deep-learningpytorchenzyme-functioncontrastive-learningai4science
      Python
      •
      Other
      •3•11•0•0•Updated May 29, 2024May 29, 2024

    • SElon7942-GEM

      Public
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•1•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
      •36•0•10•2•Updated May 8, 2024May 8, 2024
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