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I'm looking for a data set containing the over-the-counter prices of pharmaceutical drugs by pharmacy in the United States.

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It seems that this data has some business value and, hence is often available only at a cost. If a non-free solution is sufficient for you, you could try it here and here.

If it's important for you that the data comes free, you might be able to scrape it of this website which contains information for many drugs and pharmacies all over the United States but has the disadvantage that these online prices need not necessarily be in line with over-the-counter prices as there are sometimes discounts on the website. Still a good source with a lot of information.

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GoodRX has an API that you can use, easier than scraping. GoodRX Developer API

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