5 posts
A working guide to turning RNA-seq quantifications into an annotated, versioned gene table: choosing an annotation, building tx2gene, attaching biotypes and symbols, functional mapping, and cell-type annotation for single-cell data.
A working guide to going from FASTQ or a count matrix to a UMAP embedding you can defend: normalization, PCA, neighbor graph settings, initialization, and what the picture does and does not tell you.
A working guide to the FASTQ layout, naming, and read structure Cell Ranger expects, how to produce those files from BCLs, how to verify them before you burn compute, and what to do when the pipeline says it found nothing.
Why the data structure chosen for a genome, a variant set, an expression matrix, or a phylogeny decides which questions can be asked and what runs in reasonable time, prompted by a Boundary talk on coding agents.
A practical guide to building violin plots from bulk and single-cell RNA-seq counts: which normalization to plot, how to set kernel bandwidth and trimming, and how to read the shapes without fooling yourself.