rnaSentry: Guarded and Auditable Discovery of Prognostic RNA-Seq Signatures

Orchestrates the full prognostic signature pipeline from bulk RNA-seq SummarizedExperiment objects: sample-identity and quality-control auditing, confounder and design-formula detection, signature construction with cross-validation, survival modelling (Kaplan-Meier, Cox, parametric) and external validation. Every automated decision is reported with its supporting statistic and a plain-language rationale in a flag ledger and a standalone HTML report via generate_report().

Main functions

• load_counts: intake audit.

• qc_explore, sex_check: quality checks.

• design_audit, pca_audit: confounder detection.

• build_signature, km_curve, cox_model, survival_parametric, validate_external: signature and survival modelling.

• run_rnaSentry: end-to-end pipeline; lock_signature: single-use lock.

See also

Useful links:

• https://ghrieb.github.io/rnaSentry/

• https://github.com/Ghrieb/rnaSentry

• Report bugs at https://github.com/Ghrieb/rnaSentry/issues

Author

Maintainer: Abdelkarim Hani Ghrieb ghriebabdelkarimhani@gmail.com