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@ramseylab

Ramsey Laboratory at Oregon State University

Computational Systems Biology

Pinned repositories

  1. Computational elucidation of the regulatory noncoding variome

    Python 1

  2. Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)

    Java 1

  3. Web tool for managing Ramsey Lab EC2 instances

    Python

  4. Computational elucidation of the regulatory noncoding variome 3

    Python

  5. Forked from RTXteam/RTX

    Reasoning Tool RTX developed by Oregon State U. and Institute for Systems Biology

    Python

  6. Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University

    Jupyter Notebook 1

Repositories

    aws-manage

    Web tool for managing Ramsey Lab EC2 instances

    Python Apache-2.0 0 0 4 0 Updated Aug 6, 2020

    lab.saramsey.org

    Ramsey Lab website

    HTML Apache-2.0 0 0 0 0 Updated Jul 23, 2020

    vmb651

    Bioinformatics Workshop

    Jupyter Notebook Apache-2.0 0 0 0 0 Updated Apr 14, 2020

    csx46

    Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University

    Jupyter Notebook Apache-2.0 1 0 0 0 Updated Mar 12, 2020

    networkscompbio

    Code for the class CS 446/546 - Networks in computational biology

    Jupyter Notebook Apache-2.0 4 3 0 2 Updated Jan 7, 2020

    cerenkov3

    Computational elucidation of the regulatory noncoding variome 3

    Python Apache-2.0 0 0 0 0 Updated Oct 5, 2019

    RTX

    Forked from RTXteam/RTX

    Reasoning Tool RTX developed by Oregon State U. and Institute for Systems Biology

    Python MIT 7 0 0 0 Updated Jul 12, 2019

    compbio-notes

    Ramsey Lab's open notes on bioinformatics and computational biology

    Apache-2.0 0 0 0 0 Updated Jun 11, 2019

    cerenkov

    Computational elucidation of the regulatory noncoding variome

    Python Apache-2.0 0 1 2 0 Updated May 8, 2019

    gwas-llr-integrator

    Code to accompany the book chapter "Combining eQTL and SNP annotation data to identify functional noncoding SNPs in GWAS trait-associated regions"

    R Apache-2.0 0 0 0 0 Updated Mar 5, 2019

    Res2s2aM

    Code for Res2s2aM

    0 0 0 0 Updated Feb 15, 2019

    Dizzy

    Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)

    Java 0 1 0 0 Updated Apr 25, 2018

    regshape

    DNA shape-based classifier for regulatory elements (R package)

    R GPL-2.0 1 4 1 0 Updated Feb 28, 2018

    pltfbsmotif

    Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites

    MATLAB Apache-2.0 0 0 0 0 Updated Feb 27, 2018

    tlcnet

    Regulatory network reconstruction via time-lagged correlation analysis of gene expression and motif scanning data

    MATLAB Apache-2.0 0 0 0 0 Updated Dec 14, 2017

    tfbsincbeta

    Bayesian method for transcription factor binding site enrichment analysis

    R Apache-2.0 0 1 0 0 Updated Sep 10, 2016

    eqtlchiptest

    Statistical testing for overlap between expression quantitative trait loci and transcription factor location data (R code)

    R Apache-2.0 0 0 0 0 Updated Aug 14, 2016

    drugscan

    Analyze disease genes vs. transcriptome data, for in silico screening for drug repositioning (R code)

    R Apache-2.0 0 0 0 0 Updated Feb 17, 2016

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