A working pipeline for going from RNA-seq FASTQs to junction counts, PSI values, and a shortlist of splice-altering variants from your own genome, with the tools and parameters we would use.
Overnight glucose normally falls to its lowest point of the day a few hours after sleep onset. This page explains what a normal nocturnal curve looks like, how to analyze your own CGM data for real low events, and how to recognize the compression artifacts that mimic them.
Why a post-meal glucose reading in the 80s is usually a healthy result, why you can feel shaky at that number anyway, and how to tell a real reading from sensor noise using your own CGM and lab data.
A working guide to clustering bulk and single-cell RNA-seq: normalization choices that decide your dendrogram, gene-module discovery across timepoints, choosing k defensibly, and the failure modes that produce confident nonsense.
A working guide to the Bioconductor DEP and DEP2 packages for one person's mass-spectrometry proteomics. Covers import, missing values and design.
A practical guide to DNA analysis tools: what works on a 23andMe-style genotype file, what requires FASTQ/BAM/VCF from whole-genome sequencing, and the commands we would run at each step.
A practical guide to wearing a CGM without diabetes. Covers which sensors to buy, how accurate they are and what a normal glucose curve looks like.
A practical guide to Gene Ontology analysis of RNA-seq: building a defensible gene list, correcting for length and expression bias, running overrepresentation tests and GSEA in R, and collapsing redundant terms into something you can read.
A step-by-step guide to going from raw FASTQ files to an aligned CRAM, a benchmarked variant call set, an annotated shortlist, and an RNA-seq expression table, with the actual commands, parameters, and quality thresholds we use.
Read depth in RNA-seq is the number of reads assigned to your sample and, per gene, the number of reads supporting each transcript. This page explains how to compute it from your own files, why 30x means nothing here, and what depth to ask for.
A practical comparison of DeepVariant, GATK HaplotypeCaller, bcftools mpileup, Strelka2, and Clair3 for calling SNPs from your own whole-genome data, with commands, benchmarks, and the failure modes that matter.
What a blood biomarker test measures, what it costs and how to get the numbers out. Covers the math that shows whether a change between draws is real.
A working guide to turning personal RNA sequencing FASTQs into gene- and transcript-level expression estimates: reference choice, selective alignment with Salmon, spliced alignment with STAR, QC thresholds, and the checks that catch a swapped or degraded sample.
A working pipeline from FASTQ to a publication-grade expression heatmap. Covers salmon quantification, gene selection, row scaling and clustering.
A practical spec for buying whole-genome sequencing: coverage, library prep, file formats, the QC you should run yourself, and what WGS still misses.
What a post-meal glucose of 83, 87, or 94 mg/dL means, why the timing of the reading matters more than the number, and how to measure your own postprandial response properly with CGM and blood work.
Whole-genome sequencing processed with PharmCAT and Cyrius gives you more pharmacogenetic information than any branded psychiatric panel, and you keep the data. Here is how to run it and what the evidence supports.
A working guide to setting up an R and Bioconductor project around a personal molecular profile: loading your VCF, quantifying your own RNA-seq across timepoints, normalizing proteomics, and joining biomarker and glucose time series into one analyzable object.
A step-by-step guide to exporting raw genotype files from Ancestry, 23andMe, and MyHeritage, converting them to a reference-correct VCF, lifting to GRCh38, imputing, and understanding what an array file can and cannot tell you.
A working stack for analyzing your own whole-genome sequencing data: alignment with BWA-MEM2 or Dragen, variant calling with DeepVariant, annotation with VEP, and interpretation limits you should respect.