How-to

Your qPCR run is done and you have a column of Ct values. Here is how to turn them into fold changes with the ΔΔCt method, worked by hand, in a spreadsheet and in R, plus the mistakes that get qPCR figures sent back by reviewers.

Your amplicon FASTQ files are back from the sequencer, and the default CRISPResso2 numbers are already lying to you about your HDR and base editing rates. Here is how to run CRISPResso2 properly from raw paired-end reads to publication-ready allele tables.

Your DESeq2 results table has thousands of rows, and sorting it in Excel tells you almost nothing about your experiment. Here is how to build volcano plots and MA plots in R with ggplot2 — and how to read what they are actually telling you.

You can run a Western blot but you are terrified of the terminal. Here is everything a bench biologist actually needs to know about the command line — navigating files, counting sequences, searching data, and writing one-liners that replace an hour of Excel work.

You installed samtools and it broke your entire Python setup. Or DESeq2 needs R 4.3 but your system has R 4.1. Here is how Conda solves the dependency nightmare that every biologist runs into — with real commands, real installs, and real output.