If I have a single replicate per condition and I am trying to see if the differences in gene expression ( for a single gene) are significant between conditions what would be the correct test to use? Also out of curiosity, if some conditions have a single replicate while others have more than one, which test should be used then?
You're talking about comparing two numbers in a statistically significant way. I don't think that's possible.
For the second question, you may be looking for a t-test. Read more here https://compgenomr.github.io/book/how-to-test-for-differences-between-samples.html