Agent skill

Bio Epitranscriptomics Merip Preprocessing

by majiayu000 in majiayu000/claude-skill-registry

Align and QC MeRIP-seq IP and input samples for m6A analysis.

MITAuto-check passed

Install Bio Epitranscriptomics Merip Preprocessing

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/analysis/merip-preprocessing .claude/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Paste into Claude Code

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .claude/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/analysis/merip-preprocessing .agents/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .agents/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/analysis/merip-preprocessing .cursor/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .cursor/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/majiayu000/claude-skill-registry.git --path skills/analysis/merip-preprocessing

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/analysis/merip-preprocessing .gemini/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .gemini/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/analysis/merip-preprocessing .github/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .github/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install majiayu000/claude-skill-registry bio-epitranscriptomics-merip-preprocessing --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/majiayu000/claude-skill-registry.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/analysis/merip-preprocessing .opencode/skills/bio-epitranscriptomics-merip-preprocessing && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "bio-epitranscriptomics-merip-preprocessing" agent skill from https://github.com/majiayu000/claude-skill-registry/tree/main/skills/analysis/merip-preprocessing into .opencode/skills/bio-epitranscriptomics-merip-preprocessing/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-epitranscriptomics-merip-preprocessing", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: bio-epitranscriptomics-merip-preprocessing
GitHub stars: 666
Used in: 1 other repo
Token cost: ~372 tokens
SKILL.md length: 25 words
Files: 2
Skills in repo: 1,273
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Align and QC MeRIP-seq IP and input samples for m6A analysis.

Preparing MeRIP-seq data for peak calling
SKILL.md covers Alignment with STAR, QC Metrics, IP/Input Correlation and Related Skills
Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
Differential methylation analysis

What it does

Bio Epitranscriptomics Merip Preprocessing is an agent skill from majiayu000/claude-skill-registry. Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.

Its SKILL.md is about 370 tokens, which your agent loads only when the skill is triggered. The skill folder holds 1 other file (for example `metadata.json`).

The repository describes itself as: Searchable Claude Code skills catalog with source-linked guides and generated registry artifacts. The licence is MIT.

When your agent uses it

Preparing MeRIP-seq data for peak calling
Differential methylation analysis

Example prompts

“/bio-epitranscriptomics-merip-preprocessing”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 2d14a69. It shows what the files ask for, not the result of running them.

Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are bash and python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Epitranscriptomics Merip Preprocessing loads about 372 tokens when it runs. Until then it costs about 48 tokens; SKILL.md has 25 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~48
When it runs · the whole SKILL.md, loaded when a task matches: ~372

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from majiayu000/claude-skill-registry at commit 2d14a69, republished under its MIT licence (© majiayu000). 25 words, ~372 tokens.

Download SKILL.mdSave it as .claude/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md (or your agent's skills folder). This skill also uses 1 other file; get the full folder from GitHub.

name: bio-epitranscriptomics-merip-preprocessing
description: Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
tool_type: cli
primary_tool: STAR

MeRIP-seq Preprocessing

Alignment with STAR

bash

# Build index (once)
STAR --runMode genomeGenerate \
    --genomeDir star_index \
    --genomeFastaFiles genome.fa \
    --sjdbGTFfile genes.gtf

# Align IP and input samples
for sample in IP_rep1 IP_rep2 Input_rep1 Input_rep2; do
    STAR --genomeDir star_index \
        --readFilesIn ${sample}_R1.fastq.gz ${sample}_R2.fastq.gz \
        --readFilesCommand zcat \
        --outSAMtype BAM SortedByCoordinate \
        --outFileNamePrefix ${sample}_
done

QC Metrics

bash

# Index BAMs
for bam in *Aligned.sortedByCoord.out.bam; do
    samtools index $bam
done

# Check IP enrichment
# Good MeRIP: IP should have peaks, input should be uniform
samtools flagstat IP_rep1_Aligned.sortedByCoord.out.bam

IP/Input Correlation

python

import deeptools.plotCorrelation as pc

# Check replicate correlation
multiBamSummary bins \
    -b IP_rep1.bam IP_rep2.bam Input_rep1.bam Input_rep2.bam \
    -o results.npz

plotCorrelation -in results.npz \
    --corMethod spearman \
    -o correlation.png

read-qc - Raw read quality assessment
read-alignment - General alignment concepts
m6a-peak-calling - Next step after preprocessing

Files

SKILL.md and 1 other file in skills/analysis/merip-preprocessing of majiayu000/claude-skill-registry.

SKILL.md
metadata.json

Open the folder on GitHubat commit 2d14a69

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in majiayu000/claude-skill-registry, which our catalogue first saw on October 7, 2026.

BioTender-max/awesome-bio-agent-skillsskills/bioskills/merip-preprocessing

Compare with similar skills

Bio Epitranscriptomics Merip Preprocessing next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Bio Epitranscriptomics Merip Preprocessing compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Bio Epitranscriptomics Merip Preprocessing this skillmajiayu000/claude-skill-registry	666	1 repos	~372	Automated safety check: Pass	MIT	yesterday
Bio Epitranscriptomics Merip PreprocessingGPTomics/bioSkills	1.2k	1 repos	~8.5k	Automated safety check: Pass	MIT	1 mo ago
Bio Ribo Seq Riboseq PreprocessingFreedomIntelligence/OpenClaw-Medical-Skills	3.1k	1 repos	~1.3k	Automated safety check: Pass	None	2 mo ago
Bio Epitranscriptomics M6a Peak CallingGPTomics/bioSkills	1.2k	1 repos	~8.5k	Automated safety check: Pass	MIT	1 mo ago
Bio Epitranscriptomics M6a DifferentialGPTomics/bioSkills	1.2k	1 repos	~8.6k	Automated safety check: Pass	MIT	1 mo ago
Bio Clip Seq Clip AlignmentGPTomics/bioSkills	1.2k	2 repos	~5k	Automated safety check: Pass	MIT	1 mo ago

Similar skills

Bio Epitranscriptomics Merip Preprocessing
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1.2k GitHub starsUsed in 1 repo~8.5k tokens
Business, Finance & HRAuto-check passed
Bio Ribo Seq Riboseq Preprocessing
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Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment.
3.1k GitHub starsUsed in 1 repo~1.3k tokens
Writing & ContentAuto-check passed
Bio Epitranscriptomics M6a Peak Calling
GPTomics/bioSkills
Calls m6A peaks from MeRIP-seq / m6A-seq paired IP-vs-input data using exomePeak2 (transcript-aware, GC-bias-corrected Poisson GLM), MeTPeak (HMM over sliding windows), MACS3/MACS2 with --nomodel…
1.2k GitHub starsUsed in 1 repo~8.5k tokens
Research & ScienceAuto-check passed
Bio Epitranscriptomics M6a Differential
GPTomics/bioSkills
Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bamip/baminput control +…
1.2k GitHub starsUsed in 1 repo~8.6k tokens
Auto-check passed
Bio Clip Seq Clip Alignment
GPTomics/bioSkills
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware…
1.2k GitHub starsUsed in 2 repos~5k tokens
Research & ScienceAuto-check passed
Bio Clip Seq Clip Preprocessing
GPTomics/bioSkills
Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse.
1.2k GitHub starsUsed in 2 repos~4.8k tokens
Research & ScienceAuto-check passed

Questions about Bio Epitranscriptomics Merip Preprocessing

What does Bio Epitranscriptomics Merip Preprocessing do?

Align and QC MeRIP-seq IP and input samples for m6A analysis. Bio Epitranscriptomics Merip Preprocessing is an agent skill from majiayu000/claude-skill-registry. Align and QC MeRIP-seq IP and input samples for m6A analysis.

When should I use Bio Epitranscriptomics Merip Preprocessing?

Bio Epitranscriptomics Merip Preprocessing fits situations like: preparing MeRIP-seq data for peak calling; differential methylation analysis.

How do I install Bio Epitranscriptomics Merip Preprocessing in Claude Code?

Run `npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a claude-code`. Or copy the skill folder (skills/analysis/merip-preprocessing in majiayu000/claude-skill-registry) into .claude/skills/bio-epitranscriptomics-merip-preprocessing in your project. Claude Code loads it when a task matches its description.

How do I install Bio Epitranscriptomics Merip Preprocessing in Codex?

Run `npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a codex`. Or copy the skill folder (skills/analysis/merip-preprocessing in majiayu000/claude-skill-registry) into .agents/skills/bio-epitranscriptomics-merip-preprocessing in your project. Codex loads it when a task matches its description.

Can I use Bio Epitranscriptomics Merip Preprocessing in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add majiayu000/claude-skill-registry --skill bio-epitranscriptomics-merip-preprocessing -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-epitranscriptomics-merip-preprocessing, .gemini/skills/bio-epitranscriptomics-merip-preprocessing, .github/skills/bio-epitranscriptomics-merip-preprocessing and .opencode/skills/bio-epitranscriptomics-merip-preprocessing in your project.

What does Bio Epitranscriptomics Merip Preprocessing need to run?

SKILL.md names no scripts, command-line tools or credentials: Bio Epitranscriptomics Merip Preprocessing is instructions for the agent only. Our summary lists: Python 3.

Does Bio Epitranscriptomics Merip Preprocessing access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Bio Epitranscriptomics Merip Preprocessing safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Bio Epitranscriptomics Merip Preprocessing use?

Bio Epitranscriptomics Merip Preprocessing is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bio Epitranscriptomics Merip Preprocessing use?

About 372 tokens (SKILL.md is roughly 1.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Bio Epitranscriptomics Merip Preprocessing?

Skills that share tags, products or a category with Bio Epitranscriptomics Merip Preprocessing: Bio Epitranscriptomics Merip Preprocessing (GPTomics/bioSkills, 1.2k stars), Bio Ribo Seq Riboseq Preprocessing (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars), Bio Epitranscriptomics M6a Peak Calling (GPTomics/bioSkills, 1.2k stars) and Bio Epitranscriptomics M6a Differential (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bio Epitranscriptomics Merip Preprocessing?

majiayu000 (a GitHub user) maintains it in majiayu000/claude-skill-registry, which has 666 GitHub stars. The repository holds 1,273 skills in this directory. The repository was last updated on October 7, 2026.

Source: majiayu000/claude-skill-registry on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.

Bio Epitranscriptomics Merip Preprocessing

Install Bio Epitranscriptomics Merip Preprocessing

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

MeRIP-seq Preprocessing

Alignment with STAR

QC Metrics

IP/Input Correlation

Files

Used in 1 other repository

Compare with similar skills

Similar skills