Configuration

PRMeth (DecoNFlow benchmark)

Configuration as run in the cited comparison.

Overview

Configuration as run in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

2 evaluations · 11 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: PRMeth (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 PRMeth 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, D9; row 'PRMeth'; column '10M' under 'RRBS-TT'
Configuration: PRMeth (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 PRMeth 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, E9; row 'PRMeth'; column '15M' under 'RRBS-TT'
Configuration: PRMeth (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 PRMeth 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, F9; row 'PRMeth'; column '20M' under 'RRBS-TT'
Configuration: PRMeth (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 PRMeth 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, B9; row 'PRMeth'; column '2M' under 'RRBS-TT'
Configuration: PRMeth (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 PRMeth 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, C9; row 'PRMeth'; column '5M' under 'RRBS-TT'
Configuration: PRMeth (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 PRMeth 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, C10; row 'PRMeth'; column 'RRBS-TT'
Configuration: PRMeth (DecoNFlow benchmark)	Protocol: DecoNFlow WGBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark WGBS-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 PRMeth tumour-fraction LoD (WGBS-TT) ctdnameth-20261009-protocol-giuili2025-wgbs-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, H9; row 'PRMeth'; column '183M' under 'WGBS-TT'
Configuration: PRMeth (DecoNFlow benchmark)	Protocol: DecoNFlow WGBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark WGBS-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 PRMeth tumour-fraction LoD (WGBS-TT) ctdnameth-20261009-protocol-giuili2025-wgbs-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, I9; row 'PRMeth'; column '310M' under 'WGBS-TT'
Configuration: PRMeth (DecoNFlow benchmark)	Protocol: DecoNFlow WGBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark WGBS-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 PRMeth tumour-fraction LoD (WGBS-TT) ctdnameth-20261009-protocol-giuili2025-wgbs-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, J9; row 'PRMeth'; column '620M' under 'WGBS-TT'
Configuration: PRMeth (DecoNFlow benchmark)	Protocol: DecoNFlow WGBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark WGBS-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 PRMeth tumour-fraction LoD (WGBS-TT) ctdnameth-20261009-protocol-giuili2025-wgbs-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, G9; row 'PRMeth'; column '62M' under 'WGBS-TT'
Configuration: PRMeth (DecoNFlow benchmark)	Protocol: DecoNFlow WGBS-TT tumour-fraction limit of detection Dataset: DecoNFlow benchmark WGBS-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 PRMeth tumour-fraction LoD (WGBS-TT) ctdnameth-20261009-protocol-giuili2025-wgbs-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, B10; row 'PRMeth'; column 'WGBS-TT'

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Sources and history

Release 2026-10-09-8cc1db47c7f9 · Record review: source checked

3 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 1 (deconvolution and DMR tools) · Original source · bioRxiv version 1 supplementary file media-3.xlsx
Giuili et al. 2025, Supplementary Table 3 (median limit of detection) · Original source · bioRxiv version 1 supplementary file media-5.xlsx

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Technical metadata and extraction receipts

Stable ID: ctdnameth-20261009-config-giuili2025-prmeth

areas: dna-genomes
contexts: research
method types: specialist
reported name: PRMeth
foundation model eligible: false
source locator: Supplementary Table 1A row 8 ('PRMeth'); Supplementary Table 3 row label
missing metadata: version: reason: unreported; note: Supplementary Table 1A prints 'No version'
environment: container: egiuili/prmeth:v2

Related records

configuration of: PRMeth
system: PRMeth tumour-fraction LoD (RRBS-CL)
system: PRMeth tumour-fraction LoD (RRBS-TT)
system: PRMeth tumour-fraction LoD (WGBS-TT)

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