Dataset

DecoNFlow benchmark RRBS-TT in silico mixtures

In silico tumour-in-plasma read mixtures with known tumour fraction (Giuili et al. 2025).

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Release 2026-10-09-ba02f2f4a36e · Evidence verified: Not verified

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Evaluation results

10 evaluations · 60 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.0070* limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, D3; row 'CelFiE'; column '10M' under 'RRBS-TT'
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.01 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, E3; row 'CelFiE'; column '15M' under 'RRBS-TT'
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, F3; row 'CelFiE'; column '20M' under 'RRBS-TT'
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, B3; row 'CelFiE'; column '2M' under 'RRBS-TT'
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.025 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C3; row 'CelFiE'; column '5M' under 'RRBS-TT'
Configuration: CelFiE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.01 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CelFiE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C4; row 'CelFiE'; column 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, D12; row 'CIBERSORT'; column '10M' under 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, E12; row 'CIBERSORT'; column '15M' under 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, F12; row 'CIBERSORT'; column '20M' under 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, B12; row 'CIBERSORT'; column '2M' under 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C12; row 'CIBERSORT'; column '5M' under 'RRBS-TT'
Configuration: CIBERSORT (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source CIBERSORT tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C3; row 'CIBERSORT'; column 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, D11; row 'EpiDISH_RPC'; column '10M' under 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, E11; row 'EpiDISH_RPC'; column '15M' under 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.025 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, F11; row 'EpiDISH_RPC'; column '20M' under 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.25 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, B11; row 'EpiDISH_RPC'; column '2M' under 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C11; row 'EpiDISH_RPC'; column '5M' under 'RRBS-TT'
Configuration: EpiDISH_RPC (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiDISH_RPC tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C7; row 'EpiDISH_RPC'; column 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, D10; row 'EpiSCORE'; column '10M' under 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, E10; row 'EpiSCORE'; column '15M' under 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, F10; row 'EpiSCORE'; column '20M' under 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.25 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, B10; row 'EpiSCORE'; column '2M' under 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C10; row 'EpiSCORE'; column '5M' under 'RRBS-TT'
Configuration: EpiSCORE (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT 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 checked Methods, coverage and source EpiSCORE tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, C8; row 'EpiSCORE'; column 'RRBS-TT'
Configuration: EpiDISH_CP_eq (DecoNFlow benchmark)	Protocol: DecoNFlow RRBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark RRBS-TT in silico mixtures	0.01 limit-of-detection fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source EpiDISH_CP_eq tumour-fraction LoD (RRBS-TT) ctdnameth-20261009-protocol-giuili2025-rrbs-tt-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, D6; row 'EpiDISH_CP_eq'; column '10M' under 'RRBS-TT'

Source checking is not independent reproduction. Release 2026-10-09-ba02f2f4a36e.

Dataset and evaluation context

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Evidence

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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.

8 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-09-ba02f2f4a36e
Property and statement	Original source and location	Review and provenance
attributes.population 1,550 RRBS in silico mixtures: lung, prostate and colorectal tumour tissue reads (PRJNA315188) mixed into healthy plasma cfDNA reads Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.population` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
attributes.scope_note Proxy for patient plasma: tumour reads come from tissue or a cell line, not from patient cfDNA. Counts in the preprint do not reconcile: the abstract and Methods state 3,690 mixtures; the Results dataset counts (1,640, 1,550 and 440) sum to 3,630; the Methods arithmetic gives 1,600, 1,500 and 500 tumour mixtures plus 40, 50 and 50 healthy replicates (3,740). Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.scope_note` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
attributes.source_locator Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
attributes.split Five depths (2M, 5M, 10M, 15M, 20M aligned reads), ten tumour fractions from 0.01% to 50% plus 0%, ten replicates each Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
attributes.total 1550 Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.total` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
attributes.version bioRxiv version 1 (2025-11-27); mixtures generated with SillyMix v1.1.0 Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
description In silico tumour-in-plasma read mixtures with known tumour fraction (Giuili et al. 2025). Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact
name DecoNFlow benchmark RRBS-TT in silico mixtures Context-only references	A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow Original source ↗ Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D Version: bioRxiv preprint version 1, posted 2025-11-27; not peer reviewed Retrieved: 2026-10-09T19:55:30Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `1893cc9932e752a7575640dce585d5b3e3846f90626a564340c006437990adc7` Hash scope: Not reproducible by re-download: bioRxiv rewrites the PDF on each download (ModDate and XMP dates set to the download time). A copy retrieved 2026-10-09T20:21:09Z has the same length (7,728,127 bytes) and SHA-256 fa7bcf8c25532f86dc99ed7d76a13a49ae70e29ab9f46559b3e0972e86aa9b96; resetting its three date stamps to any time on that day does not give the pinned hash, so another per-download field also differs. No result value is taken from this PDF. Inspected artifact

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Release 2026-10-09-ba02f2f4a36e · Record review: source checked

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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

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Stable ID: ctdnameth-20261009-data-giuili2025-rrbs-tt-in-silico-mixtures

areas: dna-genomes
contexts: research
version: bioRxiv version 1 (2025-11-27); mixtures generated with SillyMix v1.1.0
population: 1,550 RRBS in silico mixtures: lung, prostate and colorectal tumour tissue reads (PRJNA315188) mixed into healthy plasma cfDNA reads
split: Five depths (2M, 5M, 10M, 15M, 20M aligned reads), ten tumour fractions from 0.01% to 50% plus 0%, ten replicates each
total: 1550
scope note: Proxy for patient plasma: tumour reads come from tissue or a cell line, not from patient cfDNA. Counts in the preprint do not reconcile: the abstract and Methods state 3,690 mixtures; the Results dataset counts (1,640, 1,550 and 440) sum to 3,630; the Methods arithmetic gives 1,600, 1,500 and 500 tumour mixtures plus 40, 50 and 50 healthy replicates (3,740).
source locator: Preprint Results 'Benchmarking datasets generation' (page 5); Methods; Supplementary Table 2D

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