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So I will be applying for PhD programs this fall/winter and I'm worried about my transcripts. 

GPA: 3.4

Stat GPA: 3.1 (mostly b's in my stat classes)

Calc 1 - C

Calc 2 - B+

currently taking Calc 3 and linear algebra

haven't taken the GRE yet

 

I also had two bad semesters with repeat grades which I believe are shown on my transcripts.

I guess what I'm really worried about is whether my grades in my undergrad courses will hurt my chances of acceptance. I'm applying to UC, UK, OSU, and IU. 

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hi, well for admission to Phd courses what really matters is a strong research background and good GRE score. So you haven’t lost it all. If your undergrad scores are on the lower side, make sure you compensate with a good GRE score.  Also, highlight your research projects & publications, of course, in relevant field. Further, communicate with professors under whom you want to take up research & discuss your research proposal with them. All this will certainly make your profile strong. Good Luck!

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