Recovery of known expression-outlier genes and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, OUTRIDER)
OUTRIDER with and without 100 GTEx muscle controls, scored on known loss-of-function expression genes and on true-negative samples.
No reviewed evaluations are linked here in this release. See the sources below.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Published results still to collect
This release has no source-checked evaluations linked to this page. It does not mean that the benchmark has no published results.
Charts will appear when compatible result tables have been checked against their sources.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
0 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|
No evidence rows match these filters. Choose another scope or clear the search.
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-01-28; JATS source XML
- Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Original source · medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML)
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261011-silverstein2026-protocol-expression
- areas
- rna-transcriptomes
- contexts
- clinical_research
- protocol
- Run OUTRIDER one versus all through DROP v1.2.2 at FDR 1% on each tissue cohort, and a second muscle run with 100 GTEx muscle controls added. A true positive is the known gene among reported outliers; a true-negative sample is correct only if no outlier is reported.
- version
- Table S9 (medRxiv v1 supplement)
- source locator
- Table S9 rows 7 and 8; Methods 'Expression Tools' and 'True Positive and Negative Detection'; Table S7
- limitations
- OUTRIDER + GTEx was run on muscle only (14 positives); OUTRIDER on muscle and fibroblast (15 positives).; The authors did not develop rMATS-turbo, MINTIE, FRASER, LeafcutterMD, OUTRIDER or the DROP MAE module. ANEVA-h is the authors' own method: two of its authors (K. R. Ganapathy and S. Silverstein) are the first and third authors of reference 36, the ANEVA-h preprint, so the ANEVA-H row is recorded as author_reported.; Positives are counted per known event or gene, negatives per true-negative sample: a negative sample with any reported outlier counts as one false positive. Accuracy, precision and MCC therefore mix event-level and sample-level units (Methods 'True Positive and Negative Detection').; Variants with clinically interpretable mechanisms were selected; the authors state this favours clearly defined events and likely underestimates tool sensitivity, and that binary outlier scoring of negatives may overestimate false-positive rates and lowers MCC (Discussion, limitations paragraph).; Retrospective study of a single centre's neuromuscular cohort; no confidence intervals are printed.; Table S7 true-negative rows do not reproduce Table S9 rows 7 and 8: read as in Tables S3, S4 and S8 ('YES' = no outlier), Table S7 gives OUTRIDER 8 of 9 negative samples without outliers (Table S9: 4) and OUTRIDER + GTEx 1 of 6 (Table S9: 1 of 5). The prose rates (56% and 83%) match Table S9 for OUTRIDER and Table S7 for OUTRIDER + GTEx.