Estimates cell-type composition from bulk DNA methylation and uses it to defuse the single biggest EWAS confounder. Covers reference-based deconvolution (Houseman constrained-projection, minfi estimateCellCounts2 with FlowSorted.Blood.EPIC + IDOL-optimized libraries, EpiDISH RPC/CBS/CP, 12-cell extended, cord-blood nRBC references, EpiSCORE/hepidish for solid tissue), reference-free correction (ReFACTor, RefFreeEWAS, SVA), using fractions as covariates vs the compositionality/collinearity trap, and cell-type-resolved EWAS (CellDMC, TCA, TOAST, omicwas, HIRE). Use when estimating blood/tissue cell fractions, adjusting an EWAS for composition, choosing a deconvolution reference, or attributing a methylation signal to a cell type. For the EWAS confounder-vs-mediator decision see ewas-design; for the IEAA cell-count adjustment of DNAm age see epigenetic-clocks; for clean beta input see array-preprocessing.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryEngineeringStars0
About this skill
Estimates cell-type composition from bulk DNA methylation and uses it to defuse the single biggest EWAS confounder. Covers reference-based deconvolution (Houseman constrained-projection, minfi estimateCellCounts2 with FlowSorted.Blood.EPIC + IDOL-optimized libraries, EpiDISH RPC/CBS/CP, 12-cell extended, cord-blood nRBC references, EpiSCORE/hepidish for solid tissue), reference-free correction (ReFACTor, RefFreeEWAS, SVA), using fractions as covariates vs the compositionality/collinearity trap, and cell-type-resolved EWAS (CellDMC, TCA, TOAST, omicwas, HIRE). Use when estimating blood/tissue cell fractions, adjusting an EWAS for composition, choosing a deconvolution reference, or attributing a methylation signal to a cell type. For the EWAS confounder-vs-mediator decision see ewas-design; for the IEAA cell-count adjustment of DNAm age see epigenetic-clocks; for clean beta input see array-preprocessing.
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Estimates cell-type composition from bulk DNA methylation and uses it to defuse the single biggest EWAS confounder. Covers reference-based deconvolution (Houseman constrained-projection, minfi estimateCellCounts2 with FlowSorted.Blood.EPIC + IDOL-optimized libraries, EpiDISH RPC/CBS/CP, 12-cell extended, cord-blood nRBC references, EpiSCORE/hepidish for solid tissue), reference-free correction (ReFACTor, RefFreeEWAS, SVA), using fractions as covariates vs the compositionality/collinearity trap, and cell-type-resolved EWAS (CellDMC, TCA, TOAST, omicwas, HIRE). Use when estimating blood/tissue cell fractions, adjusting an EWAS for composition, choosing a deconvolution reference, or attributing a methylation signal to a cell type. For the EWAS confounder-vs-mediator decision see ewas-design; for the IEAA cell-count adjustment of DNAm age see epigenetic-clocks; for clean beta input see array-preprocessing.
About this listing
Category
Engineering
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI