3 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 diagnosing and handling batch effects in bulk RNA-seq, from design and TMM normalization through limma, ComBat-seq, and RUV, with the checks that tell you whether the correction helped.
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.