Data Analysis Tools
The correlation between metabolite levels and gene expression
Developing Tools for Integrated Omic Analysis
The Sara Cooper Lab has generated and used a variety of large datasets for genomics and metabolomics. We spend a significant amount of time developing tools for the analysis of these datasets. Below is information about several tools we have developed. We hope you will find them useful. Please contact Dr. Cooper for any questions or additional information on using these tools.
- aRNA-pipe: A pipeline for primary analysis of RNA-sequencing data implemented for a high-performance cluster as described in Alonso et al..
- An R package for calculating proliferative index (PI) using RNA-sequencing data as described in Ramaker et al. 2017.
- An aligner for two-dimensional gas-chromatography with mass spectrometry metabolomics data implemented in R that facilitates multi-way sample comparisons and metabolite identification as described in Ramaker, Gordon, Cooper 2017.