Blog

A working guide to producing star-allele diplotypes and CPIC phenotypes from your own sequencing data with PharmCAT, Cyrius, and PyPGx, and to reading a commercial PGx report critically.

A working guide to turning RNA-seq quantifications into an annotated, versioned gene table. Covers choosing an annotation, tx2gene and biotypes.

A working pipeline from FASTQ to a ranked pathway table in R. Covers salmon, DESeq2 and fgsea, plus the confounders behind most false pathway hits.

A working transcriptome analysis workflow for one person's whole-blood RNA-seq. Covers QC, salmon quantification, normalization and pathways.

A working guide to pulling your lab results out of a patient portal as structured data, normalizing them, and analyzing them with the right statistics: reference intervals, analytical and biological variation, and reference change values.

A technical account of what a comprehensive blood panel measures, what the CMP's 14 analytes do and don't tell you, and how to get from a panel of numbers to data you can analyze yourself.

Standard continuous glucose monitors measure glucose only. Abbott's Libre Duo 10 Day adds a beta-hydroxybutyrate electrode on the same filament. Here is what each sensor measures, what the data looks like, and how to analyze it.

What is in a VCF, how to filter it down to variants worth reading and how to read a single variant end to end. Covers the limits of a negative result.

A genome kit is worth buying only if it ships you 30x PCR-free whole-genome sequencing and the underlying files. Here is the spec sheet, the QC commands to run on delivery, and what drugstore DNA kits measure.

A genome report is a filtered summary built on top of your variant calls. Here is what goes into one, which files matter more than the PDF, and what sequencing costs in 2026.

A continuous glucose monitor measures how you eat. It does not cause fat loss. What the data supports, and how to run your own meal experiments.

A working guide to HMDB's access paths: the licensed REST API, the per-record XML endpoints, and the bulk downloads. Includes a streaming parser, a DuckDB mirror, and mass-based lookup with ppm windows.

There are two products sold as a 'methylation report': an MTHFR-style SNP panel from genotyping data, and a genome-wide DNA methylation array read out as epigenetic clocks. They measure different things, and only one of them is a measurement of your current biology.

Web platforms are good at the downstream half of RNA-seq (differential expression, enrichment, plots) and bad at the upstream half (FASTQ to counts). Here is the split we'd use, with the commands, parameters, and failure modes.

A concrete walkthrough of the RNA-seq workflow from FASTQ to interpreted results: quality control, pseudoalignment with salmon, count import with tximport, differential expression with DESeq2, and the sanity checks that catch most errors.

A practical guide to adapter, quality, poly-G and poly-A trimming for RNA-seq FASTQs: which tools to use, the exact flags, how much trimming is enough, and how to verify you did not damage the data.

A working setup for looking up any SNP in your own sequencing data. Covers indexing the VCF, annotating with rsIDs and verifying genotypes in the reads.

A working pipeline for calling somatic SNVs and indels with GATK Mutect2, from BAM to annotated VCF. Covers results at low variant allele fraction.

A step-by-step guide to annotating a personal WGS VCF with Ensembl VEP. Covers cache setup, the plugin stack and consequence picking.

A practical account of continuous glucose monitor insertion, comfort, accuracy limits, and how to work with the exported data if you are not diabetic and want a metabolic baseline.