Intermediate

We’ve covered downloading data, normalization, and visualization. Now, we put it all together. This capstone post walks through a complete end-to-end analysis of a public breast cancer dataset (GSE183947) — from raw GEO download to identifying differentially expressed genes and creating a publication-ready volcano plot.

You’ve made your edit, but how much of it is actually there? This post compares the three most common ways to measure CRISPR on-target efficiency—from the "quick and dirty" T7E1 gel assay to the high-resolution precision of Amplicon NGS.

You have a gene to edit. Should you use Cas9, Cas12a, or a Base Editor? This capstone post walks you through the entire workflow—from choosing the right molecular "scissors" for your target to designing and validating your final guides.

Choosing a guide RNA that cuts your target is only half the battle. You also need one that doesn’t cut anywhere else. This post breaks down the MIT and CFD scoring systems, how off-target algorithms actually work, and which tools are best for predicting Cas9 and Cas12a off-targets.

pegRNA design has five parameters that each affect prime editing efficiency. Here are the principles behind PBS length, RT template, nick distance, and secondary structure — then how to apply them in PrimeDesign.