Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
A skill your agent uses when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue.
Install Nature Methods
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install franklee16/academic-research-skills nature-methods --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .claude/skills/nature-methods && rm -rf skills-srcUse ~/.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/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .claude/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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 install https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methodsType 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.
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install franklee16/academic-research-skills nature-methods --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .agents/skills/nature-methods && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .agents/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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.
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install franklee16/academic-research-skills nature-methods --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .cursor/skills/nature-methods && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .cursor/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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 https://github.com/franklee16/academic-research-skills.git --path Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install franklee16/academic-research-skills nature-methods --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .gemini/skills/nature-methods && rm -rf skills-srcUse ~/.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/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .gemini/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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.
$ gh skill install franklee16/academic-research-skills nature-methodsInstalls 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).
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .github/skills/nature-methods && rm -rf skills-srcUse ~/.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/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .github/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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.
$ npx skills add franklee16/academic-research-skills --skill nature-methods -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install franklee16/academic-research-skills nature-methods --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/franklee16/academic-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods .opencode/skills/nature-methods && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "nature-methods" agent skill from https://github.com/franklee16/academic-research-skills/tree/master/Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods into .opencode/skills/nature-methods/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nature-methods", 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
nature-methods- GitHub stars
- 223
- Used in
- 1 other repo
- Token cost
- ~2.2k tokens
- SKILL.md length
- 985 words
- Files
- 1
- Skills in repo
- 1,617
- Repo updated
- First seen
- Licence
- None found
At a glance
A skill your agent uses when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue.
- Targeting Nature Methods
- SKILL.md covers Journal positioning, When to trigger, Scope & topic fit and Method & evidence bar, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Deciding whether a methods/tools manuscript fits this venue
What it does
Nature Methods is an agent skill from franklee16/academic-research-skills. Use when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue. Encodes the journal's fit, framing, method-and-evidence bar, house style, official-submission re-check, and desk-reject heuristics.
Its SKILL.md is about 2.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Comprehensive collection of Claude Code skills for academic research in economics, finance, and social sciences.
When your agent uses it
- Targeting Nature Methods
- Deciding whether a methods/tools manuscript fits this venue
Example prompts
- “/nature-methods”
What it can do on your machine
Read from SKILL.md and the folder at commit 9a4b2db. 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.
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
Nature Methods loads about 2.2k tokens when it runs. Until then it costs about 61 tokens; SKILL.md has 985 words of instructions outside code blocks.
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
Without a licence we can't republish the file, so here is its outline and opening line. It has 985 words (~2,185 tokens).
“Nature Methods is the Nature Portfolio's dedicated venue for new methods, approaches, and technologies in the life sciences and related disciplines, with the distinguishing requirement that a published method must be generalizable — applicable by other researchers to their own…”
- name
- nature-methods
Files
Just SKILL.md in Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods of franklee16/academic-research-skills.
Open the folder on GitHubat commit 9a4b2db
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 franklee16/academic-research-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Nature Methods 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.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Nature Methods this skillfranklee16/academic-research-skills | 223 | 1 repos | ~2.2k | Automated safety check: Pass | None | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
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A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
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Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Related
Categories
Questions about Nature Methods
What does Nature Methods do?
A skill your agent uses when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue. Nature Methods is an agent skill from franklee16/academic-research-skills. Use when targeting Nature Methods or deciding whether a methods/tools manuscript fits this venue.
When should I use Nature Methods?
Nature Methods fits situations like: targeting Nature Methods; deciding whether a methods/tools manuscript fits this venue.
How do I install Nature Methods in Claude Code?
Run `npx skills add franklee16/academic-research-skills --skill nature-methods -a claude-code`. Or copy the skill folder (Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods in franklee16/academic-research-skills) into .claude/skills/nature-methods in your project. Claude Code loads it when a task matches its description.
How do I install Nature Methods in Codex?
Run `npx skills add franklee16/academic-research-skills --skill nature-methods -a codex`. Or copy the skill folder (Awesome-Journal-Skills-main/English-NaturalScience-Journal-Skills/skills/nature-methods in franklee16/academic-research-skills) into .agents/skills/nature-methods in your project. Codex loads it when a task matches its description.
Can I use Nature Methods 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 franklee16/academic-research-skills --skill nature-methods -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/nature-methods, .gemini/skills/nature-methods, .github/skills/nature-methods and .opencode/skills/nature-methods in your project.
What does Nature Methods need to run?
SKILL.md names no scripts, command-line tools or credentials: Nature Methods is instructions for the agent only.
Does Nature Methods 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 Nature Methods 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 Nature Methods use?
No licence was found for Nature Methods or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Nature Methods use?
About 2.2k tokens (SKILL.md is roughly 8.7k 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 Nature Methods?
Skills that share tags, products or a category with Nature Methods: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Nature Methods?
franklee16 (a GitHub user) maintains it in franklee16/academic-research-skills, which has 223 GitHub stars. The repository holds 1,617 skills in this directory. The repository was last updated on September 18, 2026.
Source: franklee16/academic-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.