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@harmslab Harms Lab @ University of Oregon

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    59 repositories

    • dataprob

      Public
      Library for fitting models using a likelihood framework.
      Python
      •
      MIT License
      •1•4•0•1•Updated Sep 18, 2024Sep 18, 2024

    • linkage

      Public
      package for fitting thermodynamic linkage models to experimental data
      Jupyter Notebook
      •
      MIT License
      •2•0•0•1•Updated Sep 17, 2024Sep 17, 2024

    • ellipticbn

      Public
      tool for measuring ellipticity of cucurbituril macrocycles
      HTML
      •
      MIT License
      •1•1•0•0•Updated Jul 16, 2024Jul 16, 2024

    • topiary

      Public
      Python framework for doing ancestral sequence reconstruction
      bioinformaticsphylogeneticsancestral-sequence-reconstructionevolutionary-biochemistrypython
      Python
      •
      MIT License
      •6•36•9•1•Updated Jul 8, 2024Jul 8, 2024

    • setup_md

      Public
      Files and scripts used to set up MD simulations in the Harms Lab
      Python
      •
      MIT License
      •1•0•0•0•Updated May 14, 2024May 14, 2024

    • eee

      Public
      ensemble epistasis engine
      Python
      •
      MIT License
      •2•0•0•0•Updated Nov 16, 2023Nov 16, 2023

    • gpseer

      Public
      A tool to predict missing data in sparsely sampled genotype-phenotype maps
      pythonstatisticsevolutionpredictionepistasisgenotype-phenotype-map
      Python
      •3•6•1•0•Updated Aug 18, 2023Aug 18, 2023

    • gpmap

      Public
      A Python API for managing genotype-phenotype map data
      geneticsevolutionnetworkxgenotype-phenotype-maps
      Python
      •8•11•1•3•Updated Aug 18, 2023Aug 18, 2023

    • epistasis

      Public
      A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.
      geneticsevolutionmodelingnonlinearepistasishigh-orderpythongenotype-phenotype-maps
      Python
      •
      The Unlicense
      •11•33•7•0•Updated Aug 18, 2023Aug 18, 2023

    • website

      Public
      Website for the lab
      HTML
      •
      MIT License
      •2•0•0•0•Updated Jan 16, 2023Jan 16, 2023

    • topiary-examples

      Public
      Jupyter notebooks demonstrating the topiary ancestral sequence reconstruction package
      Jupyter Notebook
      •
      MIT License
      •3•2•0•0•Updated Jan 3, 2023Jan 3, 2023

    • flowsym

      Public
      A Python API for simulating flow cytometry data.
      Python
      •
      MIT License
      •2•3•0•2•Updated Dec 26, 2022Dec 26, 2022

    • gpvolve

      Public
      A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.
      Python
      •
      MIT License
      •6•3•6•2•Updated Dec 26, 2022Dec 26, 2022

    • experimental-ensemble-epistasis

      Public
      Scripts and data for reproducing the analysis in "An experimental demonstration of ensemble epistasis in the lac repressor"
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • riboswitch-epistasis

      Public
      calculations and analysis files for riboswitch ensemble epistasis manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 27, 2022Oct 27, 2022

    • asr-protocol

      Public
      Protocol and scripts for doing ancestral sequence reconstruction
      Jupyter Notebook
      •
      MIT License
      •3•1•1•1•Updated Oct 3, 2022Oct 3, 2022

    • stability-constraint-ms-figures

      Public
      code to generate figures and do analyses for hS100A9/M63F stability constraint study
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 26, 2022Aug 26, 2022

    • staged-recipes

      Public
      A place to submit conda recipes before they become fully fledged conda-forge feedstocks
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5k•0•0•0•Updated Aug 7, 2022Aug 7, 2022

    • gpgraph

      Public
      NetworkX for genotype-phenotype maps
      Python
      •
      The Unlicense
      •4•1•0•1•Updated Aug 26, 2021Aug 26, 2021

    • gmx-template

      Public
      template for setting up MD simulations in the Harms lab.
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 16, 2021Apr 16, 2021

    • ensemble_epistasis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 7, 2021Apr 7, 2021

    • rosetta-docking

      Public
      scripts for doing rosetta docking calculations
      MIT License
      •1•0•0•0•Updated Mar 7, 2021Mar 7, 2021

    • m63f-biophysics

      Public
      scripts and data to reproduce biophysical investigation of S100A9/M63F
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 4, 2021Feb 4, 2021

    • were-anc-less-specific

      Public
      notebooks and scripts to reproduce analyses from "Were Ancestral Proteins Less Specific" manuscript
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Dec 8, 2020Dec 8, 2020

    • hops_enrich

      Public
      software for processing phage display data for machine learning with peplearn
      Python
      •
      The Unlicense
      •1•0•0•0•Updated Nov 29, 2020Nov 29, 2020

    • venninator

      Public
      estimate overlaps between sets
      Python
      •
      MIT License
      •1•0•0•0•Updated Nov 29, 2020Nov 29, 2020

    • vertebrate-tlr4-evolution

      Public
      scripts for reproducing vertebrate tlr4 synteny analysis
      Jupyter Notebook
      •
      The Unlicense
      •0•0•0•0•Updated Aug 26, 2020Aug 26, 2020

    • hops

      Public
      Use machine learning to find rules for peptide binding
      Jupyter Notebook
      •
      The Unlicense
      •3•7•0•1•Updated Jun 3, 2020Jun 3, 2020

    • fast_dbscan

      Public
      fast, lightweight dbscan implementation for peptide strings
      C
      •
      The Unlicense
      •2•11•0•0•Updated Apr 29, 2020Apr 29, 2020

    • gelquant

      Public
      Simple SDS-PAGE/western blot gel quantification software.
      Jupyter Notebook
      •
      MIT License
      •7•0•0•0•Updated Apr 28, 2020Apr 28, 2020