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@ramseylab Ramsey Laboratory at Oregon State University

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    27 repositories

    • lab.saramsey.org

      Public
      Ramsey Lab website
      HTML
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 5, 2025Dec 5, 2025

    • findpaths

      Public archive
      Code for finding all paths between two vertices, in a knowledge graph
      Python
      •0•1•0•0•Updated Nov 5, 2025Nov 5, 2025

    • vgrampy

      Public
      Python tools for analyzing electrochemistry voltammograms
      Python
      •1•0•1•1•Updated Aug 7, 2025Aug 7, 2025

    • vgramreg

      Public
      Exploration of regression models for processing square-wave voltammograms to estimate analyte concentration
      Python
      •0•0•0•0•Updated Apr 28, 2025Apr 28, 2025

    • wound-analysis

      Public
      Software code for the manuscript "Hybrid learning-based healing prediction from a wound image"
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Feb 20, 2024Feb 20, 2024

    • food-network

      Public
      Neo4j network of information about recipes and ingredients (h/t Rik Van Bruggen and Yong-Yeol Ahn)
      Shell
      •
      MIT License
      •0•1•0•0•Updated Jul 14, 2023Jul 14, 2023

    • ldnh

      Public
      Process square-wave voltammograms using the LDNH method
      R
      •
      MIT License
      •0•1•1•0•Updated Apr 21, 2023Apr 21, 2023

    • cs340

      Public
      Some code for the course CS340, Introduction to Databases, at Oregon State University
      Python
      •
      MIT License
      •4•1•1•0•Updated May 26, 2022May 26, 2022

    • RTX-KG2

      Public
      Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
      1•0•0•0•Updated Feb 9, 2022Feb 9, 2022

    • htsrecomb

      Public
      Code for finding putative recombination events from high-throughput sequence data from bacterial co-culture experiments
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 24, 2021Nov 24, 2021

    • cerenkov

      Public
      Computational elucidation of the regulatory noncoding variome
      Python
      •
      Apache License 2.0
      •0•1•2•0•Updated Mar 27, 2021Mar 27, 2021

    • ARAX

      Public
      Our work on the NCATS Biomedical Data Translator project.
      0•0•0•0•Updated Nov 4, 2020Nov 4, 2020

    • csx46

      Public
      Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University
      Jupyter Notebook
      •
      Apache License 2.0
      •3•15•0•0•Updated Oct 29, 2020Oct 29, 2020

    • aws-manage

      Public
      Web tool for managing Ramsey Lab EC2 instances
      Python
      •
      Apache License 2.0
      •0•1•4•0•Updated Aug 6, 2020Aug 6, 2020

    • vmb651

      Public
      Bioinformatics Workshop
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 14, 2020Apr 14, 2020

    • networkscompbio

      Public
      Code for the class CS 446/546 - Networks in computational biology
      Jupyter Notebook
      •
      Apache License 2.0
      •5•6•0•2•Updated Jan 7, 2020Jan 7, 2020

    • cerenkov3

      Public
      Computational elucidation of the regulatory noncoding variome 3
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 5, 2019Oct 5, 2019

    • RTX

      Public
      Reasoning Tool RTX developed by Oregon State U. and Institute for Systems Biology
      Python
      •
      MIT License
      •25•0•0•0•Updated Jul 12, 2019Jul 12, 2019

    • gwas-llr-integrator

      Public
      Code to accompany the book chapter "Combining eQTL and SNP annotation data to identify functional noncoding SNPs in GWAS trait-associated regions"
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Mar 5, 2019Mar 5, 2019

    • Res2s2aM

      Public
      Code for Res2s2aM
      0•0•0•0•Updated Feb 15, 2019Feb 15, 2019

    • Dizzy

      Public
      Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)
      Java
      •
      Other
      •0•1•0•0•Updated Apr 25, 2018Apr 25, 2018

    • regshape

      Public
      DNA shape-based classifier for regulatory elements (R package)
      R
      •
      GNU General Public License v2.0
      •0•5•1•0•Updated Feb 28, 2018Feb 28, 2018

    • pltfbsmotif

      Public
      Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites
      MATLAB
      •
      Apache License 2.0
      •0•0•0•0•Updated Feb 28, 2018Feb 28, 2018

    • tlcnet

      Public
      Regulatory network reconstruction via time-lagged correlation analysis of gene expression and motif scanning data
      MATLAB
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 14, 2017Dec 14, 2017

    • tfbsincbeta

      Public
      Bayesian method for transcription factor binding site enrichment analysis
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Sep 10, 2016Sep 10, 2016

    • eqtlchiptest

      Public
      Statistical testing for overlap between expression quantitative trait loci and transcription factor location data (R code)
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 15, 2016Aug 15, 2016

    • drugscan

      Public
      Analyze disease genes vs. transcriptome data, for in silico screening for drug repositioning (R code)
      R
      •
      Apache License 2.0
      •0•1•0•0•Updated Feb 17, 2016Feb 17, 2016