6 posts
A working guide to the Bioconductor DEP and DEP2 packages applied to a single person's mass-spectrometry proteomics: importing MaxQuant or DIA-NN output, handling left-censored missingness, choosing a design that survives n-of-1 sampling, and reading the result table without overclaiming.
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 for taking a personal WGS VCF into R: GDS conversion, quality metrics, ancestry PCA against 1000 Genomes, variant annotation, and polygenic score computation, with the failure modes that silently corrupt each step.
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.
How to use R and Bioconductor as the annotation, statistics, and integration layer for a personal molecular dataset: VCFs, RNA-seq counts, proteomics, and continuous glucose data, with the parts you should not do in R.
A working pipeline for taking Olink, SomaScan, or DIA-NN output into R: QC, missingness, normalization, and longitudinal within-person modeling of a single individual's plasma proteome.