local-methylation-profile
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).
npx skills add majiayu000/claude-skill-registry --skill 22-local-methylation-profile-bisnake2001-chromskills-2 --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.
# Local Methylation Profile Analysis ## Overview - **Always prompt user** for which columns in the BED files are methylation fraction/percent. Never decide by yourself. - Generat profile: Bin methylation around regions (±flank, fixed bin size), aggregate mean±SE. - Visualize: Plot mean profile with ribbon and center line. --- ## Inputs & Outputs ### Inputs ```bash methylation.bed target_regions.bed ``` ### Outputs ```bash local_methyl_profile/ stats/ CpG_around_target.tsv plots/ CpG_around_target.pdf temp/ ... # other temp file generated ``` --- ## Decision Tree ### Step 1: Preprocess input → 5-column BED (for methylKit), and 3-column BED (for target regions) ```bash awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3, $<i_methylation>}, $<i_coverage>}' methylation.bed # n is provide by user, *100 if is fraction awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3}' target_regions.bed ``` --- ### Step 2: Build methylation profiles around regions Call: - `mcp__methyl-tools__build_local_methylation_profile` with: - `methyl_bed_path`: 5-column BED-like file from preprocess_methylation. - `regions_bed_path`: 3-column BED-like file from preprocess_regions. - `output_profile_tsv_path`: path for agg
- Overview
- Inputs & Outputs
- Inputs
- Outputs
- Decision Tree
- Step 2: Build methylation profiles around regions
- Step 3: Visualization
- Parameter Guidelines
- Notes
methylation.bed
target_regions.bed
local_methyl_profile/
stats/
CpG_around_target.tsv
plots/
CpG_around_target.pdf
temp/
awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3, $<i_methylation>}, $<i_coverage>}' methylation.bed # n is provide by user, *100 if is fraction
awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3}' target_regions.bedWhat does the local-methylation-profile skill do?
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill 22-local-methylation-profile-bisnake2001-chromskills-2 --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.