Introduction | Positioning and prior art | Installation | Design decisions | Data intake | Quality control | Biological sex verification | The survival pipeline in one run | External validation | Assumptions and limitations | Avoiding common mistakes | Session info

The three-tier structure | The master impact table | Why the first failure mode is worth dwelling on | Pipeline execution on the same cohort | The LUAD honest negative (GSE31210 -> GSE50081) | Demonstrating the honest-negative concept with synthetic data | Reading this package's claims | Session info

Status note | Data | Tier 1: the naive analysis | Tier 2: rnaSentry standing guard | Risk groups | Adjusted hazard ratios | Parametric survival model | Design audit

Motivation | Build two example CSV files | Step 1: read both files | Step 2: intersect the sample IDs | Step 3: build and validate the SummarizedExperiment | Step 4: audit the design before modeling | Step 5: run the full pipeline | Assay naming: counts vs logcounts (exprs for microarray) | Session info

Status note | Setup | Tier 1: the naive analysis | Tier 2: rnaSentry standing guard | Design audit | Pairwise redundancy | Confounder scan | What the surrogate gradient looks like | Batch-adjusted screening | Tier 3: the counterfactual | Reading | Session info

Status note | Setup | Tier 1: the naive analysis | Tier 2: rnaSentry standing guard | The guardrail fires | The mean hides the spread | Tier 3: the counterfactual | Reading | Session info