Configuration

FRASER (Silverstein et al. 2026)

Configuration of FRASER: DROP v1.2.2; One versus all by tissue cohort (muscle n=71, fibroblast n=37, CHX fibroblast n=79); default parameters; FDR 5%; stranded and unstranded libraries combined.

1 evaluation · 9 results

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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))
FRASER (Silverstein et al. 2026)Evaluation	0.236	0.382	47	21	-0.588	0.5	0.309	0	21

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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'

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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-fraser

areas: rna-transcriptomes
contexts: clinical_research
method types: conventional_pipeline
reported name: FRASER
foundation model eligible: false
version: DROP v1.2.2
parameters: One versus all by tissue cohort (muscle n=71, fibroblast n=37, CHX fibroblast n=79); default parameters; FDR 5%; stranded and unstranded libraries combined
access reuse: Open-source tool; run by the authors on the NIH Biowulf cluster
source locator: Methods 'One vs All Splice Tools'; Table S9 row label
provenance note: FRASER as run in the Silverstein et al. 2026 benchmark.

Related records

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

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