For any questions or issues you can reach me by creating an issue, send me
an email (eporetsky at ucsd.edu) or on twitter (@externelly).
I am a post-doc at UC San Diego working with Alisa Huffaker and Eric Schmelz
on plant defense responses against pests and disease and I use different
bioinformatics approaches to try to answer our biological questions.
The repository still needs some work but many of the folders and sub-folders
contain more detailed README files to help reproduce the results.\
- I use a HP Z620 workstation, 16-cores (32-threads), 176gb RAM for the resource intensive analyses
- Most of the code was tested on linux but many should be compatible with mac and windows
- The Snakemake workflows were moved to a separate repository (github.com/eporetsky/workflows)
- The MutRank and syntenyZ Shiny apps are available on separate repositories
- PlantApp.org, a Dash website for comparative plant genomics, also contains downloadable gene annotations