Examining institutional data from seven cohorts of students intending to major in biology across five research-intensive institutions, this work analyzes opportunity gaps -- defined as the difference between the grade received by students from the dominant and nondominant sociodemographic groups in institutions of higher education -- at the course-section level across mathematics, physics, biology, and chemistry disciplines. From this analysis, we find that the majority of course sections have large opportunity gaps between female and male students, students who are Black, Latino/a/e/x, or indigenous to the United States and its territories and students who are White or Asian, first-generation and non-first-generation students, and low-income and non-low-income students. This work provides a framework to analyze equity across institutions using robust methodology, including: using multiple approaches to measure grades, quantile regression rankscores which adjust for previous academic performance, and cluster analysis. Recommendations are provided for institutions to identify faculty who have equitable course sections, automate equity analyses, and compare results to other institutions to make a change toward more equitable outcomes.