Workflow Standardization

Research Update – Hematodinium Investigation Yesterday’s notebook update focused on my plans to investigate future research questions. This one focuses on my current project – analyzing differential expression in Hematodinium in Grace’s samples. I’m roughly at the same stage as before – I’ve got all my differentialy-expressed GO terms, but realized a few things. The most important of those: for analysis with GO-MWU/GOseq/some other gene enrichment analysis, I need to provide all my genes, not just the differentially-expressed ones. Because of that, I had to start over on my R script that produces a newline-separated file of UniProt accessions. When going through my R script, I realized I’ve learned a lot in the last few months. The script was badly written, and I had to either sub out specific parts each time, or have differnt scripts for different files. Because of that, I decided to rewrite my scripts, and turned…

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