Package: thanatome 0.99.0

thanatome: Donor Death Signatures for Post-Mortem Control Tissue

Annotates each sample of a post-mortem tissue cohort (GTEx or similar) with its position along two transcriptional axes of donor death derived from GTEx v8 across ten tissues, ventilator (perfused versus post-mortem) and prolonged agony, plus the ischemia component of the ventilator axis. For every sample it returns a signature score per axis, a position scaled between the two reference poles of the same tissue, a state label and technical contamination flags, and optionally the fraction of the sample's deviation from the tissue centroid that lies along the axes. Samples can then be plotted, selected with explicit criteria, and the per-sample scores used as covariates in differential-expression designs or batch-correction tools. compare_controls() repeats a case-versus-control differential expression with each candidate control subset against random subsets of the same size, optionally carrying a master-regulator analysis; annotate_de() and annotate_mra() annotate existing differential-expression and regulator tables with the axes their genes fall in; audit_report() writes the summary for a supplement.

Authors:Daniel Pérez-Calixto [aut, cph], Camila Barrios-Cervantes [ctb, cph], Enrique Hernandez-Lemus [aut, cph], Hugo Tovar [aut, cre, cph], Instituto Nacional de Medicina Genómica [fnd]