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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.

Raw log2 CPM values are hard to interpret as a table. A heatmap fixes that — but the defaults are ugly. Here is how to build a publication-ready gene expression heatmap in R with pheatmap, including clustering, color palettes, and sample annotations.

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.

Raw counts from RNA-seq are not comparable across samples without normalization. Here is why that matters, what CPM and TPM actually do, and how to normalize in R.

A guide RNA score is only useful if your target base lands in the editing window. This post covers how to count protospacer positions, use BE-Designer for CBE and ABE guide design, manage bystander edits, and handle PAM constraints — with worked examples for both editor types.