integrative-DMR-DEG
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration workflows, using promoter-level methylation–expression relationships.
npx skills add majiayu000/claude-skill-registry --skill 23-integrative-dmr-deg --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.
# Integrative Methylation–Expression Correlation Analysis ## Overview This skill integrates **differential methylation** and **differential expression** datasets to reveal coordinated epigenetic regulation patterns. - Refer to **Inputs & Outputs** to verify necessary files. - **Always prompt user** for genome assembly used. - Prepare the DMR regions into 6-column standard format BED file received by HOMER. - **Annotate** the differential methylation regions to the gene promoter. - **Preprocess** differential methylation and expression tables into a standard format. - **Integrate** methylation and expression data by promoter proximity. - **Calculate correlation** between methylation change and expression fold change. - **Classify patterns** such as hypermethylation–downregulation or hypomethylation–upregulation. --- ## Inputs & Outputs ### Inputs ```bash dmr_results.txt # DMR results output by the metilene dge_result.csv # DEG results output by DESeq2 ``` ### Outputs ```bash corr_DMR_DEG/ stats/ integrated_results.tsv pattern_counts.tsv summary_stats.tsv correlation_plot.pdf temp/ homer_dmr.bed ... # Other temp files ``` --- ## Decision Tree ### Step 1: Prepare the DMR regions into
- Overview
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 2: Annotate the differential methylation regions to the gene promoter.
- Step 4: Integrate methylation and expression data by promoter proximity
dmr_results.txt # DMR results output by the metilene dge_result.csv # DEG results output by DESeq2 corr_DMR_DEG/ stats/ integrated_results.tsv pattern_counts.tsv summary_stats.tsv correlation_plot.pdf temp/ homer_dmr.bed
What does the integrative-DMR-DEG skill do?
This skill performs correlation analysis between differential methylation and differential gene expression, identifying genes with coordinated epigenetic regulation. It provides preprocessing and integration workflows, using promoter-level methylation–expression relationships.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 23-integrative-dmr-deg --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 majiayu000/claude-skill-registry, a repository with 534 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.