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bio-methylation-methylkit

Maintainer FreedomIntelligence · Last updated April 1, 2026

DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.

OpenClawNanoClawAnalysisReproductionbio-methylation-methylkit🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatindna

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-methylation-methylkit

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

R: methylKit::methRead() → filterByCoverage() → normalizeCoverage() → calculateDiffMeth().
Analyze methylation patterns across my samples" → Import per-cytosine methylation data, filter by coverage, normalize across samples, and test for differential methylation at individual CpG sites. R: methylKit::methRead() → filterByCoverage() → normalizeCoverage() → calculateDiffMeth().
getMethylationStats(meth_obj[[1]], plot = TRUE, both.strands = FALSE).

Source Doc

Excerpt From SKILL.md

Coverage per sample

getCoverageStats(meth_obj[[1]], plot = TRUE, both.strands = FALSE)


## Remove CpGs with very low or very high coverage

meth_filtered <- filterByCoverage(
    meth_obj,
    lo.count = 10,        # Minimum 10 reads
    lo.perc = NULL,
    hi.count = NULL,
    hi.perc = 99.9        # Remove top 0.1% (likely PCR artifacts)
)

Normalize coverage between samples (recommended)

meth_norm <- normalizeCoverage(meth_filtered, method = 'median')

Use cases

Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.

Not for

Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

bismark-alignment - Generate input BAM files
methylation-calling - Extract coverage files
dmr-detection - Advanced DMR methods
pathway-analysis/go-enrichment - Functional annotation

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