Evaluation

ANEVA-H on the NIH neuromuscular diagnosed RNA-seq truth set (allelic-imbalance)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

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

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)

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))
ANEVA-H (Silverstein et al. 2026)Evaluation	0.462	0.588	3	4	-0.184	0.556	0.625	1	5

All 9 result rows with coverage, uncertainty and sources

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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'

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

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

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Evaluation procedure

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)

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)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-11
dataset version: NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published
split: No split
population: 8 known allelic-imbalance genes (muscle with VCFs); 5 true-negative samples
inputs: Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters
adaptation: Not reported
metric implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix
aggregation: Sum over tissue sets
budget: Not reported
protocol id: rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split
Adaptation: Not reported
Scoring implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix

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Evidence table

Inspect claims, sources and review details

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36 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
Comparison: adaptation Not reported Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 9 ('ANEVA-H') 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: adaptation Not reported Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 9 ('ANEVA-H') 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Sum over tissue sets Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Sum over tissue sets Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 9 ('ANEVA-H') 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 9 ('ANEVA-H') 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	missing or unspecified No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters Context-only references	Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `8b987ac49f086adc0a191522436529a70f243505f7dda9926786004e15b4601c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters Context-only references	Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) Original source ↗ Table S9 row 9 ('ANEVA-H') 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 author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `3d137444b13225cf1223ad73758fdfcb4b5f772263e0aafd827d8ca57ca00120` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Benchmarking RNA-seq Tools for Real-World Diagnostic Applications (Silverstein et al., medRxiv 2026) · Original source · medRxiv preprint version 1, posted 2026-01-28; JATS source XML
Silverstein et al. 2026 Supplemental Tables S1-S10 (medRxiv media-3.xlsx) · Original source · medRxiv preprint version 1 supplement DC3 (file 344940_file09.xlsx in the JATS XML)

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Technical metadata and extraction receipts

Stable ID: rna-splicing-20261011-silverstein2026-eval-aneva-h

areas: rna-transcriptomes
contexts: clinical_research
origin: author_reported
protocol: rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance
version: Primary source as retrieved 2026-10-11
comparison: dataset version: NIH neuromuscular diagnosed RNA-seq truth set (dbGaP phs001272.v2.p1), as published; split: No split; population: 8 known allelic-imbalance genes (muscle with VCFs); 5 true-negative samples; inputs: Patient tissue RNA-seq aligned with STAR to GRCh38 (GTEx v10 pipeline); tool-specific controls as in parameters; adaptation: Not reported; metric implementation: Spreadsheet formulas over TP, FN, TN and FP (Table S9); MCC from the binary confusion matrix; aggregation: Sum over tissue sets; budget: Not reported; protocol id: rna-splicing-20261011-silverstein2026-protocol-allelic-imbalance
source locator: Table S9 row 9 ('ANEVA-H')
missing metadata: comparison.adaptation: reason: inapplicable; note: No model training or tuning on the truth set; comparison.budget: reason: unreported

Related records

system: ANEVA-H (Silverstein et al. 2026)
assessment: 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)
data: NIH neuromuscular diagnosed RNA-seq truth set (Silverstein et al. 2026)
evaluation: ANEVA-H accuracy (Silverstein et al. Table S9)
evaluation: ANEVA-H f1-score (Silverstein et al. Table S9)
evaluation: ANEVA-H false-negative-count (Silverstein et al. Table S9)
evaluation: ANEVA-H false-positive-count (Silverstein et al. Table S9)
evaluation: ANEVA-H matthews-correlation-coefficient (Silverstein et al. Table S9)
evaluation: ANEVA-H precision (Silverstein et al. Table S9)
evaluation: ANEVA-H recall (Silverstein et al. Table S9)
evaluation: ANEVA-H true-negative-count (Silverstein et al. Table S9)
evaluation: ANEVA-H true-positive-count (Silverstein et al. Table S9)

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