6 posts
A working guide to estimating immune and tissue cell-type proportions from your own bulk RNA-seq: getting the expression matrix into the right space, choosing a reference, running marker- and regression-based methods, and checking the output against a blood count.
A working guide to turning RNA-seq quantifications into an annotated, versioned gene table. Covers choosing an annotation, tx2gene and biotypes.
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.
The FASTQ layout, naming and read structure Cell Ranger expects. Covers producing the files from BCLs, verifying them and a run that finds 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.