Guarded and Auditable Discovery of Prognostic RNA-Seq Signatures

Documentation for package ‘rnaSentry’ version 0.99.19

build_signature	Build a prognostic gene signature from a survival cohort
cox_model	Adjusted Cox proportional-hazards model for a signature
design_audit	Audit candidate design covariates before differential-expression modeling
fetch_gse20685	Fetch and process GSE20685 breast cancer cohort
generate_report	Generate the rnaSentry analysis report
km_curve	Kaplan-Meier survival analysis of a signature's risk groups
load_counts	Validate and construct a SummarizedExperiment from count data
lock_signature	Lock or unlock an rnaSentry signature
pca_audit	PCA audit of expression data with optional batch association testing
plot_pca_audit	Plot PCA scores from a pca_audit result
qc_explore	Quality-control audit of a bulk RNA-seq SummarizedExperiment
run_rnaSentry	Run the complete rnaSentry pipeline
sex_check	Verify reported sex against inferred biological sex from expression
survival_parametric	Parametric survival models for a signature's risk score
validate_external	Validate a signature on an external cohort