Ramsey Laboratory at Oregon State University's repositories
lab.saramsey.org
Ramsey Lab website
wound-analysis
Software code for the manuscript "Hybrid learning-based healing prediction from a wound image"
food-network
Neo4j network of information about recipes and ingredients (h/t Rik Van Bruggen and Yong-Yeol Ahn)
RTX-KG2
Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
htsrecomb
Code for finding putative recombination events from high-throughput sequence data from bacterial co-culture experiments
ARAX
Our work on the NCATS Biomedical Data Translator project.
aws-manage
Web tool for managing Ramsey Lab EC2 instances
vmb651
Bioinformatics Workshop
networkscompbio
Code for the class CS 446/546 - Networks in computational biology
cerenkov3
Computational elucidation of the regulatory noncoding variome 3
RTX
Reasoning Tool RTX developed by Oregon State U. and Institute for Systems Biology
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"
Res2s2aM
Code for Res2s2aM
pltfbsmotif
Piecewise-linear machine-learning model for motif-based prediction of transcription factor binding sites
tlcnet
Regulatory network reconstruction via time-lagged correlation analysis of gene expression and motif scanning data
tfbsincbeta
Bayesian method for transcription factor binding site enrichment analysis
eqtlchiptest
Statistical testing for overlap between expression quantitative trait loci and transcription factor location data (R code)