bio-methylation-methylkit
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill methylkit-analysis --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Bismark 0.24+, methylKit 1.28+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # methylKit Analysis **"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()` ## Read Bismark Coverage Files ```r library(methylKit) file_list <- list('sample1.bismark.cov.gz', 'sample2.bismark.cov.gz', 'sample3.bismark.cov.gz', 'sample4.bismark.cov.gz') sample_ids <- c('ctrl_1', 'ctrl_2', 'treat_1', 'treat_2') treatment <- c(0, 0, 1, 1) # 0 = control, 1 = treatment meth_obj <- methRead( location = as.list(file_list), sample.id = as.list(sample_ids), treatment = treatment, assembly = 'hg38', context = 'CpG', pipeline = 'bismarkCoverage' ) ``` ## R
- Version Compatibility
- Read Bismark Coverage Files
- Read Bismark cytosine Report
- Basic Statistics
- Filter by Coverage
- Normalize Coverage
- Merge Samples (Unite)
- Visualize Samples
- Differential Methylation (Single CpGs)
- Tile-Based Analysis (Regions)
- Export Results
- Annotate with Genomic Features
- Reorganize for Multi-Group Comparison
- Pool Replicates
What does the bio-methylation-methylkit skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill methylkit-analysis --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.