Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 450K/EPIC hg19, intersect plus mLiftOver). Runs sample-identity QC: getSex sex prediction vs sample sheet for swap detection, rs-SNP fingerprint clustering for duplicates/swaps, and Sentrix chip/array-position batch diagnosis. Use when filtering methylation array probes, detecting sample swaps or mislabels, collapsing EPICv2 replicates, or merging 450K/EPIC/EPICv2 cohorts. For IDAT-to-corrected-beta normalization see array-preprocessing; for batch correction and study design see ewas-design.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
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About this skill
Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 450K/EPIC hg19, intersect plus mLiftOver). Runs sample-identity QC: getSex sex prediction vs sample sheet for swap detection, rs-SNP fingerprint clustering for duplicates/swaps, and Sentrix chip/array-position batch diagnosis. Use when filtering methylation array probes, detecting sample swaps or mislabels, collapsing EPICv2 replicates, or merging 450K/EPIC/EPICv2 cohorts. For IDAT-to-corrected-beta normalization see array-preprocessing; for batch correction and study design see ewas-design.
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Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 450K/EPIC hg19, intersect plus mLiftOver). Runs sample-identity QC: getSex sex prediction vs sample sheet for swap detection, rs-SNP fingerprint clustering for duplicates/swaps, and Sentrix chip/array-position batch diagnosis. Use when filtering methylation array probes, detecting sample swaps or mislabels, collapsing EPICv2 replicates, or merging 450K/EPIC/EPICv2 cohorts. For IDAT-to-corrected-beta normalization see array-preprocessing; for batch correction and study design see ewas-design.
About this listing
Category
General
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