Package: rnaSentry Type: Package Title: Guarded and Auditable Discovery of Prognostic RNA-Seq Signatures Version: 0.99.19 Authors@R: person("Abdelkarim Hani", "Ghrieb", email = "ghriebabdelkarimhani@gmail.com", role = c("aut", "cre")) Description: Orchestrates the statistical pipeline underlying prognostic biomarker discovery from bulk RNA-seq SummarizedExperiment objects: sample-identity and quality-control auditing, confounder and design-formula detection prior to differential expression, signature construction with explicit cross-validation stability reporting, survival modeling (Kaplan-Meier, log-rank, Cox proportional hazards), and external validation against public cohorts. Every automated statistical decision is reported with its supporting statistic and a plain-language rationale, and validation stages are gated rather than silently degraded when guardrail criteria are not met. The package records all guardrail decisions, flag ledgers, and validation results in a structured audit trail that can be rendered into a standalone HTML report. License: MIT + file LICENSE Encoding: UTF-8 RoxygenNote: 7.3.3 Depends: R (>= 4.5.0) Imports: S4Vectors, SummarizedExperiment, survival, withr, methods Suggests: Biobase, BiocParallel, BiocStyle, GEOquery, ggplot2, knitr, rmarkdown, testthat (>= 3.0.0) VignetteBuilder: knitr Config/testthat/edition: 3 biocViews: Software, GeneExpression, RNASeq, DifferentialExpression, Survival, QualityControl, BatchEffect, Normalization URL: https://ghrieb.github.io/rnaSentry/, https://github.com/Ghrieb/rnaSentry BugReports: https://github.com/Ghrieb/rnaSentry/issues Config/pak/sysreqs: zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-10-01 13:05:47 UTC RemoteUrl: https://github.com/bioc/rnaSentry RemoteRef: HEAD RemoteSha: d445c42b8e8e27d93769b0a7483f6c4ac7135c7b NeedsCompilation: no Packaged: 2026-10-02 17:46:24 UTC; root Author: Abdelkarim Hani Ghrieb [aut, cre] Maintainer: Abdelkarim Hani Ghrieb