Anti-Defensive Writing Editor
Kiterlin/anti-defensive-writing
Edits drafts to strip needless caveats, hedges and disclaimers while keeping the limits that matter for accuracy, ethics, law, safety and method.
Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved…
Install Vdjdb Publish
$ npx skills add antigenomics/vdjdb-db --skill vdjdb-publish -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-publish --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-publish .claude/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .claude/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publishType 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-publish -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-publish --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-publish .agents/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .agents/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publish -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-publish --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-publish .cursor/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .cursor/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publish--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-publish -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-publish --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-publish .gemini/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .gemini/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publishInstalls 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-publish -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-publish .github/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .github/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publish -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-publish --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-publish .opencode/skills/vdjdb-publish && 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-publish" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-publish into .opencode/skills/vdjdb-publish/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-publish", 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-publish- GitHub stars
- 157
- Token cost
- ~2k tokens
- SKILL.md length
- 1,025 words
- Files
- 1
- Skills in repo
- 8
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved…
- Works in 5 steps: Reconcile the submission → Check readiness → Commit data separately → …
- A chunk is ready to publish
- SKILL.md covers 1. Reconcile the submission, 2. Check readiness, 3. Commit data separately and 4. Validate the combined…, plus 2 more sections
- Calls uv and git
What it does
Vdjdb Publish is an agent skill from 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 observations and optional metadata follow-ups. Use when a chunk is ready to publish or an imported paper needs closeout.
Its SKILL.md is about 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 Writing & Content, covering Copy editing and proofreading. It works with PubMed. The repository describes itself as: Git-based antigen specificity database storage & management.
When your agent uses it
- A chunk is ready to publish
- An imported paper needs closeout
Example prompts
- “/vdjdb-publish”
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- Reconcile the submission
- Check readiness
- Commit data separately
- Validate the combined candidate
- Merge and close out
What it can do on your machine
Read from SKILL.md and the folder at commit aba357e. 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
Shell commands in SKILL.md call:
uvgit
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use uv and git, which can reach the network depending on how they are called.
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 Publish loads about 2k tokens when it runs. Until then it costs about 81 tokens; SKILL.md has 1,025 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 1,025 words (~2,011 tokens).
“Read AUTHORITIES.md and the submission guide. Use existing batch authorization throughout; ask only for a new decision outside that scope.”
- name
- vdjdb-publish
Files
Just SKILL.md in skills/vdjdb-publish of antigenomics/vdjdb-db.
Open the folder on GitHubat commit aba357e
Compare with similar skills
Vdjdb Publish 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 Publish this skillantigenomics/vdjdb-db | 157 | — | ~2k | Automated safety check: Pass | Custom licence | |
| Anti-Defensive Writing EditorKiterlin/anti-defensive-writing | 875 | — | ~3.5k | Automated safety check: Pass | MIT | |
| Academic Writing Assistantdonghuixin/AI-Vibe-Writing-Skills | 497 | — | ~616 | Automated safety check: Pass | MIT | |
| Academic Prose De-AI Editorheise3/academic-deai | 254 | — | ~1.4k | Automated safety check: Pass | MIT | |
| Academic Paper PolishHKUSTDial/Supervisor-Skills | 8.8k | — | ~3.1k | Automated safety check: Pass | CC-BY-NC-SA-4.0 | |
| Review PaperIngar30/reviewer | 222 | — | ~1.8k | Automated safety check: Pass | MIT |
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Academic Prose De-AI Editor
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Academic Paper Polish
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Polishes academic prose without changing its meaning: grammar and flow fixes, tone matched to the evidence, AI-tone removal and Chinese-to-English rewriting for submission.
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…
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Validate VDJdb build code, CI, output contracts and release promotions against a released corpus.
Vdjdb Duplicates
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Review repeated paired receptor-pMHC observations and metadata synonyms within and across VDJdb publications, preserving distinct experiments and reports.
Vdjdb Extract
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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
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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
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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…
Vdjdb Structures
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Extract and proofread deposited TCR-pMHC observations with the local tcren pipeline, then update the PDB aggregate chunk.
Related
Works with
Categories
Questions about Vdjdb Publish
What does Vdjdb Publish do?
Publish proofread VDJdb chunks through dev, reconcile publication issues, preserve record identity, keep validation changes separate, and close completed imports while tracking unresolved…. Vdjdb Publish is an agent skill from 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 observations and optional metadata follow-ups.
When should I use Vdjdb Publish?
Vdjdb Publish fits situations like: A chunk is ready to publish; an imported paper needs closeout.
How do I install Vdjdb Publish in Claude Code?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-publish -a claude-code`. Or copy the skill folder (skills/vdjdb-publish in antigenomics/vdjdb-db) into .claude/skills/vdjdb-publish in your project. Claude Code loads it when a task matches its description.
How do I install Vdjdb Publish in Codex?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-publish -a codex`. Or copy the skill folder (skills/vdjdb-publish in antigenomics/vdjdb-db) into .agents/skills/vdjdb-publish in your project. Codex loads it when a task matches its description.
Can I use Vdjdb Publish 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-publish -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-publish, .gemini/skills/vdjdb-publish, .github/skills/vdjdb-publish and .opencode/skills/vdjdb-publish in your project.
What does Vdjdb Publish need to run?
Going by SKILL.md and its folder, Vdjdb Publish needs the command-line tools its instructions call (uv and git).
Does Vdjdb Publish access the network?
SKILL.md contains no URLs. Its commands use uv and git, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Vdjdb Publish 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 Publish use?
Vdjdb Publish 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 Publish use?
About 2k tokens (SKILL.md is roughly 8k 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 Publish?
Skills that share tags, products or a category with Vdjdb Publish: Anti-Defensive Writing Editor (Kiterlin/anti-defensive-writing, 875 stars), Academic Writing Assistant (donghuixin/AI-Vibe-Writing-Skills, 497 stars), Academic Prose De-AI Editor (heise3/academic-deai, 254 stars) and Academic Paper Polish (HKUSTDial/Supervisor-Skills, 8.8k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Vdjdb Publish?
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 10, 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.