Pinned Repositories
ARAX
Our work on the NCATS Biomedical Data Translator project.
cerenkov3
Computational elucidation of the regulatory noncoding variome 3
cs340
Some code for the course CS340, Introduction to Databases, at Oregon State University
csx46
Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University
Dizzy
Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)
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"
ldnh
Process square-wave voltammograms using the LDNH method
networkscompbio
Code for the class CS 446/546 - Networks in computational biology
regshape
DNA shape-based classifier for regulatory elements (R package)
RTX-KG2
Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
Ramsey Laboratory at Oregon State University's Repositories
ramseylab/csx46
Code for the 2020 class Networks in Computational Biology (CS446/546) at Oregon State University
ramseylab/networkscompbio
Code for the class CS 446/546 - Networks in computational biology
ramseylab/regshape
DNA shape-based classifier for regulatory elements (R package)
ramseylab/cerenkov
Computational elucidation of the regulatory noncoding variome
ramseylab/cs340
Some code for the course CS340, Introduction to Databases, at Oregon State University
ramseylab/Dizzy
Framework for stochastic kinetic modeling of biochemical reaction networks (Java code)
ramseylab/drugscan
Analyze disease genes vs. transcriptome data, for in silico screening for drug repositioning (R code)
ramseylab/food-network
Neo4j network of information about recipes and ingredients (h/t Rik Van Bruggen and Yong-Yeol Ahn)
ramseylab/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"
ramseylab/ldnh
Process square-wave voltammograms using the LDNH method
ramseylab/tfbsincbeta
Bayesian method for transcription factor binding site enrichment analysis
ramseylab/ARAX
Our work on the NCATS Biomedical Data Translator project.
ramseylab/cerenkov3
Computational elucidation of the regulatory noncoding variome 3
ramseylab/RTX-KG2
Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
ramseylab/aws-manage
Web tool for managing Ramsey Lab EC2 instances
ramseylab/eqtlchiptest
Statistical testing for overlap between expression quantitative trait loci and transcription factor location data (R code)
ramseylab/htsrecomb
Code for finding putative recombination events from high-throughput sequence data from bacterial co-culture experiments
ramseylab/lab.saramsey.org
Ramsey Lab website
ramseylab/pltfbsmotif
Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites
ramseylab/Res2s2aM
Code for Res2s2aM
ramseylab/RTX
Reasoning Tool RTX developed by Oregon State U. and Institute for Systems Biology
ramseylab/tlcnet
Regulatory network reconstruction via time-lagged correlation analysis of gene expression and motif scanning data
ramseylab/vmb651
Bioinformatics Workshop
ramseylab/wound-analysis
Software code for the manuscript "Hybrid learning-based healing prediction from a wound image"