Dataset

NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)

RNA-seq from 97 previously diagnosed samples of patients with pediatric neuromuscular disease: 76 true-positive samples from 68 probands with confirmed aberrant RNA events and 21 true-negative samples with pathogenic variants not expected to change RNA.

Evaluation results

7 evaluations · 63 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.462 Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell F9, row 'ANEVA-H', column 'Accuracy'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.588 F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell I9, row 'ANEVA-H', column 'F1'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	3 False negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell C9, row 'ANEVA-H', column 'False Negatives'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	4 False positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell E9, row 'ANEVA-H', column 'False Positives'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	-0.184 MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell J9, row 'ANEVA-H', column 'MCC'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.556 Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell G9, row 'ANEVA-H', column 'Precision'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.625 Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell H9, row 'ANEVA-H', column 'Recall'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	1 True negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell D9, row 'ANEVA-H', column 'True Negatives'
Configuration: ANEVA-H (Silverstein et al. 2026)	Protocol: Recovery of known allelic-imbalance genes and outlier calls in true-negative samples, patient muscle RNA-seq (Silverstein et al. Table S9, ANEVA-H and MAE) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	5 True positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance) rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell B9, row 'ANEVA-H', column 'True Positives'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.236 Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell F4, row 'FRASER', column 'Accuracy'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.382 F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell I4, row 'FRASER', column 'F1'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	47 False negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell C4, row 'FRASER', column 'False Negatives'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	21 False positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell E4, row 'FRASER', column 'False Positives'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	-0.588 MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell J4, row 'FRASER', column 'MCC'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.5 Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell G4, row 'FRASER', column 'Precision'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.309 Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell H4, row 'FRASER', column 'Recall'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0 True negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell D4, row 'FRASER', column 'True Negatives'
Configuration: FRASER (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	21 True positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell B4, row 'FRASER', column 'True Positives'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.273 Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell F5, row 'FRASER2.0', column 'Accuracy'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.2 F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell I5, row 'FRASER2.0', column 'F1'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	14 False negatives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell C5, row 'FRASER2.0', column 'False Negatives'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	2 False positives (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) count · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell E5, row 'FRASER2.0', column 'False Positives'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	-0.241 MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell J5, row 'FRASER2.0', column 'MCC'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.5 Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell G5, row 'FRASER2.0', column 'Precision'
Configuration: FRASER2.0 (Silverstein et al. 2026)	Protocol: Recovery of known pathogenic splicing events and outlier calls in true-negative samples, patient RNA-seq (Silverstein et al. Table S9, splicing tools) Dataset: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)	0.125 Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source FRASER2.0 on the NIH neuromuscular diagnosed RNA-seq truth set (splicing) rna-splicing-20261011-silverstein2026-protocol-splicing Aggregation: Not reported Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026); Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Table S9 (sheet 'Table S9') cell H5, row 'FRASER2.0', column 'Recall'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Readiness checks, gaps and artifacts

Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

Evidence incomplete

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Verified: Not verified

Evidence incomplete

Investigate discrepancies

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

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Missing or unresolved evidence

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File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
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Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

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Evidence

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Evidence table

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16 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Assay Short-read RNA-seq of skeletal muscle, cultured fibroblasts and cycloheximide-treated fibroblasts, sequenced in small batches over 14 years with mixed stranded and unstranded libraries; GTEx v10 pipeline, STAR v2.7.10a, GRCh38 (GENCODE 39) Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Assay Short-read RNA-seq of skeletal muscle, cultured fibroblasts and cycloheximide-treated fibroblasts, sequenced in small batches over 14 years with mixed stranded and unstranded libraries; GTEx v10 pipeline, STAR v2.7.10a, GRCh38 (GENCODE 39) Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.assay` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population 97 diagnosed samples; 68 true-positive splicing variants (16 muscle, 7 fibroblast, 45 cycloheximide-treated fibroblast), 15 expression true-positive genes and 8 allelic-imbalance true-positive genes; 21 true-negative samples. Tool cohorts mixed diagnosed and undiagnosed samples by tissue (muscle n=71, fibroblast n=37, cycloheximide-treated fibroblast n=79). Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Population 97 diagnosed samples; 68 true-positive splicing variants (16 muscle, 7 fibroblast, 45 cycloheximide-treated fibroblast), 15 expression true-positive genes and 8 allelic-imbalance true-positive genes; 21 true-negative samples. Tool cohorts mixed diagnosed and undiagnosed samples by tissue (muscle n=71, fibroblast n=37, cycloheximide-treated fibroblast n=79). Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Reuse restrictions Controlled access through dbGaP phs001272.v2.p1 Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.reuse_restrictions` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Reuse restrictions Controlled access through dbGaP phs001272.v2.p1 Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.reuse_restrictions` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; retrospective detection of known events Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1, posted 2026-01-28; JATS source XML Retrieved: 2026-10-11T21:38:32Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split No split; retrospective detection of known events Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML) Retrieved: 2026-10-11T21:38:52Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-silverstein2026-data-nih-neuromuscular-diagnosed-rnaseq

areas: rna-transcriptomes
contexts: clinical_research
version: As published (dbGaP phs001272.v2.p1)
assay: Short-read RNA-seq of skeletal muscle, cultured fibroblasts and cycloheximide-treated fibroblasts, sequenced in small batches over 14 years with mixed stranded and unstranded libraries; GTEx v10 pipeline, STAR v2.7.10a, GRCh38 (GENCODE 39)
population: 97 diagnosed samples; 68 true-positive splicing variants (16 muscle, 7 fibroblast, 45 cycloheximide-treated fibroblast), 15 expression true-positive genes and 8 allelic-imbalance true-positive genes; 21 true-negative samples. Tool cohorts mixed diagnosed and undiagnosed samples by tissue (muscle n=71, fibroblast n=37, cycloheximide-treated fibroblast n=79).
split: No split; retrospective detection of known events
reuse restrictions: Controlled access through dbGaP phs001272.v2.p1
source locator: Methods 'Patient Recruitment', 'RNA-seq Alignment', 'True Positive Definition', 'True Negative Definition' and 'One vs All Splice Tools'; Results 'Truth set selection'; Tables S3 to S8; Data Availability

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