Baseline: Select a patient-RNA splicing-variant validation workflow
Baseline of Select a patient-RNA splicing-variant validation workflow
FRASER and OUTRIDER, with a legacy splice-site vote
Baseline method for the use case, reviewed against its cited sources.
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field baseline Context-only references | Detection of aberrant splicing events in RNA-seq data using FRASER amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:23:57.289375+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field baseline Context-only references | saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 27:103, published online 2026-02-18; PMC13019952 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field baseline Context-only references | Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids3 values
| Detection of aberrant splicing events in RNA-seq data using FRASER amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:23:57.289375+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids3 values
| saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 27:103, published online 2026-02-18; PMC13019952 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Method ids3 values
| Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| Detection of aberrant splicing events in RNA-seq data using FRASER amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:23:57.289375+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 27:103, published online 2026-02-18; PMC13019952 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records4 values
| Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Rationale On patient RNA, FRASER (splicing) and OUTRIDER (expression) are the standard outlier callers, run in the DROP workflow; they fit count models to the cohort and are not trained on labelled variants. On DNA, the reference is the Legacy Ensemble, a vote across MaxEntScan, NNSplice, GeneSplicer and a SpliceSiteFinder-style matrix; NNSplice is an early neural network, so this vote is a legacy comparator rather than a strictly pre-machine-learning one. Context-only references | Detection of aberrant splicing events in RNA-seq data using FRASER amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC fullTextXML retrieved 2026-10-07T12:23:57.289375+00:00 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
3 source records and release history
- Detection of aberrant splicing events in RNA-seq data using FRASER · Original source · Europe PMC fullTextXML retrieved 2026-10-07T12:23:57.289375+00:00
- saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval · Original source · Genome Biology 27:103, published online 2026-02-18; PMC13019952 full-text XML
- Analyzing the performance of deep learning splice prediction algorithms (Fortier, Rudy and Scherer, PLOS One 2026) · Original source · PLOS One 21(5):e0348885, published 2026-05-13; PMC13170886 full-text XML
Technical metadata and extraction receipts
Stable ID: use-case-baseline-patient-rna-splicing-validation
- field
- baseline
- value
- FRASER and OUTRIDER, with a legacy splice-site vote
- source locator
- amp-oncology-rna-20261007-source-pmc7822922: Results (beta-binomial outlier test, denoising autoencoder, DROP workflow); rna-splicing-20261009-source-segers2026: Background (FRASER as state of the art, and OUTRIDER, OutSingle and FRASER); rna-splicing-20261011-fortier2026-source-article: Methods (Legacy Ensemble N-of-4 vote) and Introduction (NNSplice and machine learning)
- method ids
- rna-splicing-20261009-method-fraser; rna-splicing-20261009-method-outrider; rna-splicing-20261011-fortier2026-method-legacy-ensemble
- rationale
- On patient RNA, FRASER (splicing) and OUTRIDER (expression) are the standard outlier callers, run in the DROP workflow; they fit count models to the cohort and are not trained on labelled variants. On DNA, the reference is the Legacy Ensemble, a vote across MaxEntScan, NNSplice, GeneSplicer and a SpliceSiteFinder-style matrix; NNSplice is an early neural network, so this vote is a legacy comparator rather than a strictly pre-machine-learning one.
- review
- method: source-hash-verification; automated-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that proposed the baseline; no human review claimed; reviewed at: 2026-10-12T18:00:00Z; note: Reviewer corrected value and rationale and source list. Sources re-retrieved and read; method records and their configuration links checked against the use case's active comparisons. Names the reference newer methods are compared with, not a recommendation. See docs/reviews/use-cases/baselines-2026-10-12.md.
- pins
- record id: amp-oncology-rna-20261007-source-pmc7822922; fields: status; attributes.artifact_sha256; sha256: bd7e82c3608d41aa8da0e2a6c2053e5ba1f5cae0a4ed9b0e3dbd853e2965d8cc; record id: rna-splicing-20261009-source-segers2026; fields: status; attributes.artifact_sha256; sha256: 1ccf092301c812c7f1c03608214280563a10a3c6e416acac5c9f48bf545ca2ec; record id: rna-splicing-20261011-fortier2026-source-article; fields: status; attributes.artifact_sha256; sha256: f632aac0a971c54f908ad18bc9965d498c05b69bd07552d9915807db55a22233; record id: use-case-patient-rna-splicing-validation; fields: status; name; description; facets; attributes.question; attributes.decision; attributes.inputs; attributes.output; attributes.exclusions; attributes.setting; attributes.clinical_scope; attributes.intended_users; sha256: b85cad56e15fbfad66a2e70c3b193ed56c464e5e44b62a19b12f391e409ec897