rewirebio.iobenchmarks
Protocol

Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)

Variant-level classification of experimentally tested splicing effect by DNA-based splice predictors.

8 evaluations · 56 results

Overview

Variant-level classification of experimentally tested splicing effect by DNA-based splice predictors.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

8 recorded evaluations, 56 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

8 evaluations · 56 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.832 f1-score
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F38; row AtLeast1, column F1
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.871 negative-predictive-value
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H38; row AtLeast1, column Neg Pred Value
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.731 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G38; row AtLeast1, column Pos Pred Value
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.731 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E38; row AtLeast1, column Precision
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.966 recall
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C38; row AtLeast1, column Sensitivity (Recall)
Configuration: At least 1 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.391 specificity
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 1 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D38; row AtLeast1, column Specificity
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.878 f1-score
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F39; row AtLeast2, column F1
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.831 negative-predictive-value
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H39; row AtLeast2, column Neg Pred Value
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.844 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G39; row AtLeast2, column Pos Pred Value
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.844 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E39; row AtLeast2, column Precision
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.915 recall
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C39; row AtLeast2, column Sensitivity (Recall)
Configuration: At least 2 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.71 specificity
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 2 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D39; row AtLeast2, column Specificity
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.856 f1-score
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F40; row AtLeast3, column F1
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.737 negative-predictive-value
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H40; row AtLeast3, column Neg Pred Value
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.883 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G40; row AtLeast3, column Pos Pred Value
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.883 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E40; row AtLeast3, column Precision
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.831 recall
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C40; row AtLeast3, column Sensitivity (Recall)
Configuration: At least 3 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.812 specificity
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 3 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D40; row AtLeast3, column Specificity
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.76 f1-score
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell F41; row AtLeast4, column F1
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.6 negative-predictive-value
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell H41; row AtLeast4, column Neg Pred Value
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.927 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell G41; row AtLeast4, column Pos Pred Value
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.927 precision
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell E41; row AtLeast4, column Precision
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.644 recall
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell C41; row AtLeast4, column Sensitivity (Recall)
Configuration: At least 4 of 4 splice predictors (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.913 specificity
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

At least 4 of 4 splice predictors on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S4 'In House dataset', cell D41; row AtLeast4, column Specificity
Configuration: Pangolin (Drost et al.)Protocol: Splice-effect prediction against patient-RNA or exon-trapping results, in-house diagnostic cohort (Drost et al. Data S1)
Dataset: Drost et al. in-house RNA-tested diagnostic variants, scorable subset
0.939 auprc
fraction · higher

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

Pangolin on in-house scorable variants (count not printed)

rna-splicing-20261009-protocol-drost2025-inhouse

Aggregation: Not reported

Routine RNA-based analysis of potential splicing variants facilitates genomic diagnostics and reveals limitations of in silico prediction tools; Drost et al. 2025, Data S1 (Tables S1-S6) · Data S1 Table S3 'Stratified datasets', Dataset 'In House', cell I12; row Pangolin, column AUPRC

Source checking is not independent reproduction. Release 2026-10-10-7b8f80935f90.

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.

Author-reported evaluations
4
External evaluations
4

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set class prior where supervised fitting is permitted

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

Regularised classifier on simple permitted features, or protocol's conventional reference

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 2026-10-10-7b8f80935f90. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

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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

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Evidence table

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Sources and history

Release 2026-10-10-7b8f80935f90 · Record review: source checked

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261009-protocol-drost2025-inhouse

areas
dna-genomes
contexts
clinical_research
protocol
Score each variant with SpliceAI, Pangolin, SPiP and SQUIRLS; truth is the experimental result in patient RNA (RT-PCR and Sanger) or exon trapping (effect on splicing versus no effect). AUROC (plotROC) and AUPRC (yardstick) from continuous scores; sensitivity, specificity, precision, F1, PPV and NPV (caret) after binarising at literature thresholds (SQUIRLS 0.018, SPiP 0.452, Pangolin 0.106, SpliceAI 0.12), and for at-least-N consensus rules.
version
Data S1 Tables S3 and S4
source locator
Data S1 Table S3 'Stratified datasets', Dataset 'In House' (F12:I15); Table S4 'In House dataset' (B32:H41)
limitations
Ascertainment: 87% of in-house variants were sent for RNA testing because Alamut predicted a splicing change, so negatives are mostly predicted-but-unconfirmed variants.; Restricted to variants scorable by all four tools; per-tool missing scores are not counted as negatives.; Variant-level splicing effect, not pathogenicity; tissue was chosen per gene (blood, fibroblasts or exon trapping), not modelled by the predictors.; Literature thresholds, not tuned on this set; AUROC/AUPRC have no printed uncertainty.
missing metadata
metric implementation: reason: unextracted; note: R code not published with the article; packages plotROC 2.3.1, yardstick 1.2.0 and caret 6.0.94 are named
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