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    86 repositories

    • Snekmer

      Public
      Pipeline to apply encoded Kmer analysis to protein sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•25•3•Updated Oct 1, 2024Oct 1, 2024

    • spammR

      Public
      Spatial Analysis of Multiomics Measurement in R
      R
      •
      Other
      •0•5•11•0•Updated Sep 27, 2024Sep 27, 2024

    • AML_sorted_proteomics

      Public
      R
      •
      MIT License
      •1•0•0•0•Updated Sep 27, 2024Sep 27, 2024

    • coderdata

      Public
      Automation scripts and benchmark dataset package for cancer drug prediction deep learning models.
      deep-learningcancerdrug-responsebenchmark-datasetmachine-learning
      Jupyter Notebook
      •
      Other
      •3•11•30•0•Updated Sep 27, 2024Sep 27, 2024

    • 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
      •1•2•6•2•Updated Sep 23, 2024Sep 23, 2024

    • srpAnalytics

      Public
      This repository contains the code necessary to process any new data for the Superfund Research Program Analytics Portal.
      R
      •
      MIT License
      •0•5•4•0•Updated Sep 20, 2024Sep 20, 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
      •3•3•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
      •28•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
      •2•7•8•1•Updated Mar 5, 2024Mar 5, 2024

    • ML_UVvisModels

      Public
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •1•11•1•0•Updated Feb 20, 2024Feb 20, 2024

    • emll

      Public
      some code for linlog model simulation
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •6•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
      •4•15•4•0•Updated Jan 15, 2024Jan 15, 2024

    • EinsumNetworks

      Public
      Python
      •20•0•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
      •41•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

    • AVine-GEM

      Public
      azotobacter_vinelandii_dj
      Jupyter Notebook
      •0•0•0•0•Updated Sep 1, 2023Sep 1, 2023

    • ConsortiumModels

      Public
      Jupyter Notebook
      •0•0•3•1•Updated Aug 30, 2023Aug 30, 2023

    • ion-mob-ms

      Public
      Workflow for analyzing ion mobility ms-ms data
      Python
      •
      BSD 2-Clause "Simplified" License
      •0•1•10•0•Updated Jul 25, 2023Jul 25, 2023

    • cytokineDrugResistance

      Public
      Studying the impacts of cytokines on drug resistance in AML
      HTML
      •
      MIT License
      •2•1•2•0•Updated Jun 30, 2023Jun 30, 2023

    • CLEAN

      Public
      CLEAN: a contrastive learning model for high-quality functional prediction of proteins
      Python
      •
      MIT License
      •41•0•0•0•Updated Jun 27, 2023Jun 27, 2023

    • foldseek

      Public
      Foldseek enables fast and sensitive comparisons of large structure sets.
      C
      •
      GNU General Public License v3.0
      •99•0•0•0•Updated Jun 25, 2023Jun 25, 2023