R

A table of log2 CPM values is hard to read. 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.

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.

GEO has thousands of published RNA-seq datasets — including the one from that paper you just read. This post shows you how to pull any GEO dataset into R with GEOquery, extract the count matrix and sample metadata, and save both as CSVs for downstream analysis.

Six steps from raw CSV to a publication-ready figure with significance bars. A complete, copy-paste-ready R workflow using dplyr, ggplot2, and ggsignif — built on the qPCR dataset from Arc 1.

t.test() and aov() replace ten minutes of clicking in GraphPad Prism. Here is how to run t-tests, ANOVA, and post-hoc comparisons on your qPCR data — with code you can actually reproduce.