DecoNFlow RRBS-CL tumour-fraction limit of detection
Median limit of detection of the tumour fraction for reference-based deconvolution tools on the RRBS-CL mixtures.
Overview
Median limit of detection of the tumour fraction for reference-based deconvolution tools on the RRBS-CL mixtures.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
5 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
5 evaluations · 30 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.001 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, M3; row 'CelFiE'; column '10M' under 'RRBS-CL' |
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.001 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, N3; row 'CelFiE'; column '15M' under 'RRBS-CL' |
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.001 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, O3; row 'CelFiE'; column '20M' under 'RRBS-CL' |
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.0010* limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, K3; row 'CelFiE'; column '2M' under 'RRBS-CL' |
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.001 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, L3; row 'CelFiE'; column '5M' under 'RRBS-CL' |
| Configuration: CelFiE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.001 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceCelFiE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet B, D4; row 'CelFiE'; column 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, M11; row 'EpiDISH_RPC'; column '10M' under 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, N11; row 'EpiDISH_RPC'; column '15M' under 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, O11; row 'EpiDISH_RPC'; column '20M' under 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, K11; row 'EpiDISH_RPC'; column '2M' under 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, L11; row 'EpiDISH_RPC'; column '5M' under 'RRBS-CL' |
| Configuration: EpiDISH_RPC (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_RPC tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet B, D7; row 'EpiDISH_RPC'; column 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.05 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, M10; row 'EpiSCORE'; column '10M' under 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.05 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, N10; row 'EpiSCORE'; column '15M' under 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.05 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, O10; row 'EpiSCORE'; column '20M' under 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.1 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, K10; row 'EpiSCORE'; column '2M' under 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.05 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, L10; row 'EpiSCORE'; column '5M' under 'RRBS-CL' |
| Configuration: EpiSCORE (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.05 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiSCORE tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet B, D8; row 'EpiSCORE'; column 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, M6; row 'EpiDISH_CP_eq'; column '10M' under 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, N6; row 'EpiDISH_CP_eq'; column '15M' under 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, O6; row 'EpiDISH_CP_eq'; column '20M' under 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.007 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, K6; row 'EpiDISH_CP_eq'; column '2M' under 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, L6; row 'EpiDISH_CP_eq'; column '5M' under 'RRBS-CL' |
| Configuration: EpiDISH_CP_eq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_eq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet B, D5; row 'EpiDISH_CP_eq'; column 'RRBS-CL' |
| Configuration: EpiDISH_CP_ineq (DecoNFlow benchmark) | Protocol: DecoNFlow RRBS-CL tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-CL in silico mixtures | 0.003 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceEpiDISH_CP_ineq tumour-fraction LoD (RRBS-CL) ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod Aggregation: Not reported A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow; Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Supplementary Table 3 sheet A, M5; row 'EpiDISH_CP_ineq'; column '10M' under 'RRBS-CL' |
Source checking is not independent reproduction. Release 2026-10-09-8cc1db47c7f9.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- CelFiE tumour-fraction LoD (RRBS-CL)
- CIBERSORT tumour-fraction LoD (RRBS-CL)
- EpiDISH_RPC tumour-fraction LoD (RRBS-CL)
- EpiSCORE tumour-fraction LoD (RRBS-CL)
- EpiDISH_CP_eq tumour-fraction LoD (RRBS-CL)
- EpiDISH_CP_ineq tumour-fraction LoD (RRBS-CL)
- MetDecode tumour-fraction LoD (RRBS-CL)
- meth_atlas tumour-fraction LoD (RRBS-CL)
- PRMeth tumour-fraction LoD (RRBS-CL)
- UXM tumour-fraction LoD (RRBS-CL)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- External evaluations
- 5
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-09-8cc1db47c7f9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
Inspect claims, sources and review details
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Sources and history
Release 2026-10-09-8cc1db47c7f9 · Record review: source checked
2 source records and release history
- A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow · Original source · bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed
- Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Original source · bioRxiv version 1 supplementary file media-5.xlsx
Technical metadata and extraction receipts
Stable ID: ctdnameth-20261009-protocol-giuili2025-rrbs-cl-tumour-fraction-lod
- areas
- dna-genomes
- contexts
- research
- protocol
- Build a reference of tumour and healthy cfDNA samples, select the top 250 hypomethylated DMRs per entity (adjusted p < 0.01) with each of limma, DMRfinder and wgbstools, deconvolve every mixture with each tool, then compute the limit of detection per combination. Lowest tumour fraction at which the estimated fractions of the ten replicates are significantly higher than those of 0% tumour samples (one-tailed unpaired Mann-Whitney U test, Benjamini-Hochberg adjusted p < 0.01), moving from higher to lower fractions; tested grid 0.0001, 0.001, 0.003, 0.007, 0.01, 0.025, 0.05, 0.1, 0.25, 0.5.
- version
- Preprint version 1, Methods 'Evaluation metrics and missing values'; DecoNFlow v2.2.0
- metric
- limit-of-detection
- metric direction
- lower
- unit
- fraction
- unit detail
- Tumour DNA fraction of the mixture (0.007 means 0.7%)
- aggregation
- Median over the combinations analysed (tumour types and DMR selection tools); the pooled combinations are not listed in the table
- limitations
- In silico mixtures, not patient plasma.; Values are medians on a discrete grid of tested fractions; medians can fall between grid points.; The table does not state which combinations each median pools.; Preprint, not peer reviewed.
- source locator
- Preprint Methods 'Evaluation metrics and missing values' (pages 26-27) and Figure 4 legend; Supplementary Table 3
Related records
- uses data: DecoNFlow benchmark RRBS-CL in silico mixtures
- assessment: CelFiE tumour-fraction LoD (RRBS-CL)
- assessment: CIBERSORT tumour-fraction LoD (RRBS-CL)
- assessment: EpiDISH_RPC tumour-fraction LoD (RRBS-CL)
- assessment: EpiSCORE tumour-fraction LoD (RRBS-CL)
- assessment: EpiDISH_CP_eq tumour-fraction LoD (RRBS-CL)
- assessment: EpiDISH_CP_ineq tumour-fraction LoD (RRBS-CL)
- assessment: MetDecode tumour-fraction LoD (RRBS-CL)
- assessment: meth_atlas tumour-fraction LoD (RRBS-CL)
- assessment: PRMeth tumour-fraction LoD (RRBS-CL)
- assessment: UXM tumour-fraction LoD (RRBS-CL)
- assessed by: Select a plasma ctDNA methylation detection workflow