LeafcutterMD (Silverstein et al. 2026)
Configuration of LeafCutterMD: version v0.2.9; One versus all by tissue cohort; LeafCutter intron clusters (min 50 split reads per cluster, max intron 500 kb); groups with >= 20 reads; FDR 5%.
Overview
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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)) |
|---|---|---|---|---|---|---|---|---|---|
| LeafcutterMD (Silverstein et al. 2026)Evaluation | 0 | 0 | 67 | 21 | -1 | 0 | 0 | 0 | 0 |
All 9 result rows with coverage, uncertainty and sources
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How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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)
Technical metadata and extraction receipts
Stable ID: rna-splicing-20261011-silverstein2026-config-leafcuttermd
- areas
- rna-transcriptomes
- contexts
- clinical_research
- method types
- conventional_pipeline
- reported name
- LeafcutterMD
- foundation model eligible
- false
- version
- v0.2.9
- parameters
- One versus all by tissue cohort; LeafCutter intron clusters (min 50 split reads per cluster, max intron 500 kb); groups with >= 20 reads; FDR 5%
- 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
- LeafcutterMD as run in the Silverstein et al. 2026 benchmark.
Related records
- configuration of: LeafCutterMD
- system: LeafcutterMD on the NIH neuromuscular diagnosed RNA-seq truth set (splicing)