# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "thanatome" in publications use:'
type: software
license: MIT
title: 'thanatome: Donor Death Signatures for Post-Mortem Control Tissue'
version: 0.99.0
abstract: 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:
- family-names: Pérez-Calixto
  given-names: Daniel
  email: dperez@inmegen.gob.mx
  orcid: https://orcid.org/0009-0004-3988-1260
- family-names: Hernandez-Lemus
  given-names: Enrique
  email: ehernandez@inmegen.gob.mx
  orcid: https://orcid.org/0000-0002-1872-1397
- family-names: Tovar
  given-names: Hugo
  email: hatovar@inmegen.gob.mx
  orcid: https://orcid.org/0000-0002-8360-6133
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/hachepunto/thanatome
commit: 2abb737d23d7d0df1124caa5af3213ef055280bc
url: https://github.com/hachepunto/thanatome
date-released: '2026-11-09'
contact:
- family-names: Tovar
  given-names: Hugo
  email: hatovar@inmegen.gob.mx
  orcid: https://orcid.org/0000-0002-8360-6133