4 posts
A working transcriptome analysis workflow for a single person's whole-blood RNA-seq: QC, selective-alignment quantification with salmon, gene-level counts, normalization across timepoints, cell-composition correction, and pathway interpretation.
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: building the count matrix, filtering, size factors, dispersion, Wald versus likelihood ratio tests, log fold change shrinkage, and the sanity checks that catch most mistakes.