{ "_id": "6af27e6ff58eaab799206cb5", "Package": "thanatome", "Title": "Donor Death Signatures for Post-Mortem Control Tissue", "Version": "0.99.0", "Authors@R": "c(\nperson(\"Daniel\", \"Pérez-Calixto\",\nemail = \"dperez@inmegen.gob.mx\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0009-0004-3988-1260\")),\nperson(\"Camila\", \"Barrios-Cervantes\",\nemail = \"paulacamilabarrioscervantes@gmail.com\",\nrole = c(\"ctb\", \"cph\"),\ncomment = c(ORCID = \"0009-0006-9971-790X\")),\nperson(\"Enrique\", \"Hernandez-Lemus\",\nemail = \"ehernandez@inmegen.gob.mx\",\nrole = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-1872-1397\")),\nperson(\"Hugo\", \"Tovar\",\nemail = \"hatovar@inmegen.gob.mx\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0002-8360-6133\")),\nperson(\"Instituto Nacional de Medicina Genómica\", role = \"fnd\",\ncomment = c(ROR = \"https://ror.org/01qjckx08\",\nproject = \"INMEGEN-2026-14, Proyecto 81\")))", "Description": "Annotates each sample of a post-mortem tissue cohort (GTEx\nor similar) with its position along two transcriptional axes of\ndonor death derived from GTEx v8 across ten tissues, ventilator\n(perfused versus post-mortem) and prolonged agony, plus the\nischemia component of the ventilator axis. For every sample it\nreturns a signature score per axis, a position scaled between\nthe two reference poles of the same tissue, a state label and\ntechnical contamination flags, and optionally the fraction of\nthe sample's deviation from the tissue centroid that lies along\nthe axes. Samples can then be plotted, selected with explicit\ncriteria, and the per-sample scores used as covariates in\ndifferential-expression designs or batch-correction tools.\ncompare_controls() repeats a case-versus-control differential\nexpression with each candidate control subset against random\nsubsets of the same size, optionally carrying a\nmaster-regulator analysis; annotate_de() and annotate_mra()\nannotate existing differential-expression and regulator tables\nwith the axes their genes fall in; audit_report() writes the\nsummary for a supplement.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "biocViews": "Software, QualityControl, Transcriptomics, RNASeq,\nGeneExpression, BatchEffect, Classification,\nDifferentialExpression, Sequencing", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "URL": "https://github.com/hachepunto/thanatome", "BugReports": "https://github.com/hachepunto/thanatome/issues", "LazyData": "false", "Date": "2026-11-09", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-11-09 23:33:37 UTC", "RemoteUrl": "https://github.com/BiocStaging/thanatome", "RemoteRef": "HEAD", "RemoteSha": "2abb737d23d7d0df1124caa5af3213ef055280bc", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-10 01:56:05 UTC", "User": "root" }, "Author": "Daniel Pérez-Calixto [aut, cph] (ORCID:\n),\nCamila Barrios-Cervantes [ctb, cph] (ORCID:\n),\nEnrique Hernandez-Lemus [aut, cph] (ORCID:\n),\nHugo Tovar [aut, cre, cph] (ORCID:\n),\nInstituto Nacional de Medicina Genómica [fnd] (ROR:\n, project: INMEGEN-2026-14, Proyecto 81)", "Maintainer": "Hugo Tovar ", "_user": "biocstaging", "_type": "src", "_file": "thanatome_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/d5dada75f97f51cdf8d9ff740ff46dd8b7a3b7e3af7e704cf56a5a0b88b123c4", "_filesize": 1415562, "_sha256": 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