Comparing drug-binding affinity of different drugs to different transcription factors

I am trying to analyze 5 different drug candidates on >1000 candidate genes as therapeutic targets.
My raw data has a few columns: Gene, Annotation Sequence, Binding Intensity (3 replicates, so I have 3 columns for this value per each drug and gene), Average Binding Intensity. I’m not really sure where the best place to start is. I am thinking about doing basic one-way ANOVA across the 3 different drugs and getting the p-value, but I’m not sure how to do this in R given that I have 3 technical replicates for each drug. Additionally, do you have any suggestions on which direction I should take this analysis?

e.g.

Gene. Annotation Sequence. Drug 1 (replicate 1). Drug 1 (replicate 2). Drug 1 (replicate 3). ….
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