UMR-LMR-PMD-detection
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. The pipeline provides high-resolution enhancer-like LMRs, promoter-associated UMRs, and large-scale PMDs characteristic of reprogramming, aging, or cancer methylomes, enabling integration with chromatin accessibility, TF binding, and genome architecture analyses.
npx skills add majiayu000/claude-skill-registry --skill 26-umr-lmr-pmd-detection --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.
# Unmethylated Regions (UMR) & Low-Methylated Region (LMR) & Partially Methylated Domain (PMD) Detection ## 1. Overview This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. Main steps include: - Refer to the **Inputs & Outputs** section to check available inputs and design the output structure. - **Always prompt user** for genome assembly used. - **Always prompt user** for which columns are methylation fraction/percent and coverage and strand. - Convert BED → GRanges with mC/nC counts. - Perform CpG filtering (coverage threshold). - Call UMRs/LMRs using MethylSeekR segmentation. - Mask UMR/LMR and detect PMDs using a 2-state HMM (optional). - Export annotations as BED files and summary tables. --- ## 2. When to Use This Skill ### Biological questions Use this skill when your research aims to: - Identify enhancer-like hypomethylated domains (LMRs). - Detect large-scale methylation erosion (PMDs). - Quantify global methylation heterogeneity. - Explore regulatory element accessibility fr
- 1. Overview
- 2. When to Use This Skill
- Biological questions
- 3. Inputs & Outputs
- Inputs
- Outputs
- 4. Decision Tree
- Step 1: Prepare the object for detecting UMR/LMR/PMD
- Step 2: UMR and LMR detection
- Step 3: PMD detection
- Notes & troubleshooting
LMR_PMD_calling/ regions/ UMRs.bed/ LMRs.bed/ PMDs.bed/
What does the UMR-LMR-PMD-detection skill do?
This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls. The pipeline provides high-resolution enhancer-like LMRs, promoter-associated UMRs, and large-scale PMDs characteristic of reprogramming, aging, or cancer methylomes, enabling integration with chromatin accessibility, TF binding, and genome architecture analyses.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 26-umr-lmr-pmd-detection --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.