6 posts
A working guide to gene set enrichment analysis on personal RNA-seq: building a defensible ranked list with DESeq2, running fgsea against MSigDB, reading the enrichment plot, and using GSVA when you have no contrast.
A working pipeline from a counts matrix to a ranked, deduplicated pathway table for personal RNA-seq, including the n=1 designs that are valid, the blood cell composition problem, and which tools to trust.
A working transcriptome analysis workflow for one person's whole-blood RNA-seq. Covers QC, salmon quantification, normalization and pathways.
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 working pipeline from salmon quantification files to a differential expression table and pathway results, written for one person's longitudinal blood transcriptome rather than a two-group lab experiment.
A working guide to running DESeq2 on bulk RNA-seq counts. Covers the count matrix, dispersion, shrinkage and the sanity checks that catch most mistakes.