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JimLiu/baoyu-skills
Reformats plain text or Markdown articles with frontmatter, a title, a summary, headings, bold, lists and code blocks, and saves a separate formatted copy.
Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions…
Install Vdjdb Format
$ npx skills add antigenomics/vdjdb-db --skill vdjdb-format -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-format --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/antigenomics/vdjdb-db.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/vdjdb-format .claude/skills/vdjdb-format && 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 "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .claude/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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/antigenomics/vdjdb-db/tree/master/skills/vdjdb-formatType 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 antigenomics/vdjdb-db --skill vdjdb-format -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-format --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/antigenomics/vdjdb-db.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/vdjdb-format .agents/skills/vdjdb-format && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .agents/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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 antigenomics/vdjdb-db --skill vdjdb-format -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-format --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/antigenomics/vdjdb-db.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/vdjdb-format .cursor/skills/vdjdb-format && 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 "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .cursor/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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/antigenomics/vdjdb-db.git --path skills/vdjdb-format--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 antigenomics/vdjdb-db --skill vdjdb-format -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-format --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/antigenomics/vdjdb-db.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/vdjdb-format .gemini/skills/vdjdb-format && 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 "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .gemini/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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 antigenomics/vdjdb-db vdjdb-formatInstalls 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 antigenomics/vdjdb-db --skill vdjdb-format -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/antigenomics/vdjdb-db.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/vdjdb-format .github/skills/vdjdb-format && 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 "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .github/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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 antigenomics/vdjdb-db --skill vdjdb-format -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-format --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/antigenomics/vdjdb-db.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/vdjdb-format .opencode/skills/vdjdb-format && 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 "vdjdb-format" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-format into .opencode/skills/vdjdb-format/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-format", 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
vdjdb-format- GitHub stars
- 157
- Token cost
- ~976 tokens
- SKILL.md length
- 447 words
- Files
- 1
- Skills in repo
- 8
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions…
- Tasks that involve CSV and tabular files
- SKILL.md covers Name the publication, Inspect assembly before editing and Preserve frequency and assay…
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Tasks that involve Copy editing and proofreading
What it does
Vdjdb Format is an agent skill from antigenomics/vdjdb-db. Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions, IPD-IMGT/HLA and murine H2 MHC allele names, species CamelCase, method vocabulary, reference id prefixes - and write a format log naming the authority behind every change. Use after vdjdb-extract and before vdjdb-proofread, or on any TSV whose gene or allele spellings need bringing to IMGT.
Its SKILL.md is about 980 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 Documents & Office, covering CSV and tabular files and Copy editing and proofreading. The repository describes itself as: Git-based antigen specificity database storage & management.
When your agent uses it
- Tasks that involve CSV and tabular files
- Tasks that involve Copy editing and proofreading
Example prompts
- “/vdjdb-format”
What it can do on your machine
Read from SKILL.md and the folder at commit 5dfc25f. 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
Vdjdb Format loads about 976 tokens when it runs. Until then it costs about 123 tokens; SKILL.md has 447 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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 447 words (~976 tokens).
“Read AUTHORITIES.md. Use the current chunk specification and a shipping header rather than positional column numbers or copied column lists.”
- name
- vdjdb-format
Files
Just SKILL.md in skills/vdjdb-format of antigenomics/vdjdb-db.
Open the folder on GitHubat commit 5dfc25f
Compare with similar skills
Vdjdb Format 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 |
|---|---|---|---|---|---|---|
| Vdjdb Format this skillantigenomics/vdjdb-db | 157 | — | ~976 | Automated safety check: Pass | Custom licence | |
| Markdown Article FormatterJimLiu/baoyu-skills | 26k | 7 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Module Authoringdna-seq/just-dna-lite | 141 | — | ~4.8k | Automated safety check: Notes | AGPL-3.0 | |
| Chinese Official Document Draftingzhaohui-yang/official-document-drafting | 140 | — | ~1.5k | Automated safety check: Pass | MIT | |
| Review PaperIngar30/reviewer | 222 | — | ~1.8k | Automated safety check: Pass | MIT | |
| Chinese Official Document QAzhaohui-yang/official-document-drafting | 140 | — | ~466 | Automated safety check: Pass | Custom licence |
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Chinese Official Document Drafting
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Drafts, rewrites and standardizes Chinese official documents and formal reports such as notices, requests and meeting minutes, and exports the result to Word.
Review Paper
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Review an attached academic economics paper PDF with independent specialist audits and a complete evidence-grounded report, resume an interrupted paper review, or export a completed Reviewer report…
Chinese Official Document QA
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Checks the structure and quality of a finished Chinese official document with a section-checking script and a manual checklist, without rewriting it.
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More from antigenomics/vdjdb-db
All 8 skills in this repoVdjdb Publish
antigenomics/vdjdb-db
Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved…
Vdjdb Build Integrity
antigenomics/vdjdb-db
Validate VDJdb build code, CI, output contracts and release promotions against a released corpus.
Vdjdb Duplicates
antigenomics/vdjdb-db
Review repeated paired receptor-pMHC observations and metadata synonyms within and across VDJdb publications, preserving distinct experiments and reports.
Vdjdb Extract
antigenomics/vdjdb-db
Extract TCR:pMHC specificity records from raw submission sources - supplementary XLS/CSV tables, PDF manuscripts, 10x Genomics contig and clonotype files, AIRR Rearrangement TSVs, Adaptive ImmunoSEQ…
Vdjdb Harmonize
antigenomics/vdjdb-db
Canonicalise antigen.gene and antigen.species in a VDJdb chunk against the epitope dictionary and the gene and species alias tables, detect spurious values (UniProt descriptions, "[species]"…
Vdjdb Proofread
antigenomics/vdjdb-db
Validate a VDJdb chunk with vdjdb qc and vdjdb submission, explain every finding with a specific suggested fix and the authority behind it, resolve method-field and MHC problems the rules cannot…
Related
Questions about Vdjdb Format
What does Vdjdb Format do?
Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions…. Vdjdb Format is an agent skill from antigenomics/vdjdb-db. Normalise the controlled-vocabulary fields of a raw VDJdb chunk TSV to the form the database records - IMGT V/D/J gene and allele names including Adaptive ImmunoSEQ and Arden conversions, IPD-IMGT/HLA and murine H2 MHC allele names, species CamelCase, method vocabulary, reference id prefixes - and write a format log naming the authority behind every change.
When should I use Vdjdb Format?
Vdjdb Format fits situations like: tasks that involve CSV and tabular files; tasks that involve Copy editing and proofreading.
How do I install Vdjdb Format in Claude Code?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-format -a claude-code`. Or copy the skill folder (skills/vdjdb-format in antigenomics/vdjdb-db) into .claude/skills/vdjdb-format in your project. Claude Code loads it when a task matches its description.
How do I install Vdjdb Format in Codex?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-format -a codex`. Or copy the skill folder (skills/vdjdb-format in antigenomics/vdjdb-db) into .agents/skills/vdjdb-format in your project. Codex loads it when a task matches its description.
Can I use Vdjdb Format 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 antigenomics/vdjdb-db --skill vdjdb-format -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/vdjdb-format, .gemini/skills/vdjdb-format, .github/skills/vdjdb-format and .opencode/skills/vdjdb-format in your project.
What does Vdjdb Format need to run?
SKILL.md names no scripts, command-line tools or credentials: Vdjdb Format is instructions for the agent only.
Does Vdjdb Format 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 Vdjdb Format 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 Vdjdb Format use?
Vdjdb Format has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Vdjdb Format use?
About 976 tokens (SKILL.md is roughly 3.9k 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 Vdjdb Format?
Skills that share tags, products or a category with Vdjdb Format: Markdown Article Formatter (JimLiu/baoyu-skills, 26k stars), Module Authoring (dna-seq/just-dna-lite, 141 stars), Chinese Official Document Drafting (zhaohui-yang/official-document-drafting, 140 stars) and Review Paper (Ingar30/reviewer, 222 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Vdjdb Format?
antigenomics (a GitHub organization) maintains it in antigenomics/vdjdb-db, which has 157 GitHub stars. The repository holds 8 skills in this directory. The repository was last updated on October 7, 2026.
Source: antigenomics/vdjdb-db on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.