Configuration

rMATS (Silverstein et al. 2026)

rMATS: version v4.1.2; Each patient against ten GTEx tissue-matched controls; --novelSS --allow-clipping; -mel 700; FDR 5%; all five MATS event files assessed.

1 evaluation · 9 results

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

Evaluations and results

1 evaluation · 9 results. Different protocols are not a single leaderboard.

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)

Sorted by Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9)) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Accuracy (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	F1 (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	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))	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))	MCC (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	Precision (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	Recall (positives per known event or gene, negatives per true-negative sample; aggregated across the tissue sets each tool was run on (Table S9))	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))	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))
rMATS (Silverstein et al. 2026)Evaluation	0.469	0.638	8	9	-0.361	0.625	0.652	0	15

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: rMATS (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)	0.469 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 rMATS 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 F2, row 'rMATS', column 'Accuracy'
Configuration: rMATS (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)	0.638 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 rMATS 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 I2, row 'rMATS', column 'F1'
Configuration: rMATS (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)	8 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 rMATS 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 C2, row 'rMATS', column 'False Negatives'
Configuration: rMATS (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)	9 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 rMATS 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 E2, row 'rMATS', column 'False Positives'
Configuration: rMATS (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)	-0.361 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 rMATS 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 J2, row 'rMATS', column 'MCC'
Configuration: rMATS (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)	0.625 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 rMATS 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 G2, row 'rMATS', column 'Precision'
Configuration: rMATS (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)	0.652 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 rMATS 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 H2, row 'rMATS', column 'Recall'
Configuration: rMATS (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 rMATS 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 D2, row 'rMATS', column 'True Negatives'
Configuration: rMATS (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)	15 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 rMATS 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 B2, row 'rMATS', column 'True Positives'

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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-config-rmats

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: rMATS
foundation model eligible: false
version: v4.1.2
parameters: Each patient against ten GTEx tissue-matched controls; --novelSS --allow-clipping; -mel 700; FDR 5%; all five MATS event files assessed
access reuse: Open-source tool; run by the authors on the NIH Biowulf cluster
source locator: Methods 'Case vs Control Splice Tools'; Table S9 row label
provenance note: rMATS as run in the Silverstein et al. 2026 benchmark.

Related records

configuration of: rMATS-turbo
system: rMATS on the NIH neuromuscular diagnosed RNA-seq truth set (splicing)

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