I'm Deepa Rao, a computational microbial ecologist, oceanographer, and science communicator.
My GitHub site is a portfolio of analysis and useful code from lab experiments, field observations, and models.
Code in Python & R.
- Cultured algae under a matrix of iron and vitamin B12 concentrations to examine its metabolic response to dual nutrient limitation
- Analyzed proteomic data to identify significantly differentially abundant proteins using the power law global error model (PLGEM) approach (citation)
- Calculated metrics to compare normalized protein abundances across treatments; in this example, the low iron treatments -/+ B12.
- Using Bokeh, I customized code to generate MA plots (log2 average vs. log2 fold change) of proteins between two treatments, as well as the 1:1 line for comparison.
- Highlighted specific protein categories: significantly differentially abundant (DAP), B12, iron (Fe), and cell cycle.
- Included hover-text to aid visual inspection of individual proteins (a few thousand in this figure), to connect the data with protein annotation and ORF id.
- Embedded Bokeh .html figure onto GitHub pages site for portfolio.