Geo Fetch
ClawBio/ClawBio
Query metadata and download data from the NCBI Gene Expression Omnibus (GEO).
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…
Install Vdjdb Extract
$ npx skills add antigenomics/vdjdb-db --skill vdjdb-extract -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-extract --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-extract .claude/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .claude/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extractType 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-extract -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-extract --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-extract .agents/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .agents/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extract -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-extract --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-extract .cursor/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .cursor/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extract--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-extract -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install antigenomics/vdjdb-db vdjdb-extract --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-extract .gemini/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .gemini/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extractInstalls 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-extract -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-extract .github/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .github/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extract -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-extract --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-extract .opencode/skills/vdjdb-extract && 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-extract" agent skill from https://github.com/antigenomics/vdjdb-db/tree/master/skills/vdjdb-extract into .opencode/skills/vdjdb-extract/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "vdjdb-extract", 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-extract- GitHub stars
- 157
- Token cost
- ~1.2k tokens
- SKILL.md length
- 592 words
- Files
- 1
- Skills in repo
- 8
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
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…
- Submitter folder has to become a chunk file
- SKILL.md covers Reconcile the sources, Preserve the submitted biology and Record methods and provenance
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
- Before vdjdb-format and vdjdb-proofread
What it does
Vdjdb Extract is an agent skill from 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 exports - into a VDJdb chunk TSV, verifying every extracted sequence, gene, allele and reference id back against the source. Use when a paper, dataset or submitter folder has to become a chunk file, before vdjdb-format and vdjdb-proofread.
Its SKILL.md is about 1.2k 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 Documents & Office, covering CSV and tabular files, Bioinformatics and Copy editing and proofreading. The repository describes itself as: Git-based antigen specificity database storage & management.
When your agent uses it
- Submitter folder has to become a chunk file
- Before vdjdb-format and vdjdb-proofread
Example prompts
- “/vdjdb-extract”
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 Extract loads about 1.2k tokens when it runs. Until then it costs about 113 tokens; SKILL.md has 592 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 592 words (~1,232 tokens).
“Read AUTHORITIES.md and the chunk specification. Respect the requested source and technology scope. A reference already present in VDJdb does not establish complete coverage.”
- name
- vdjdb-extract
Files
Just SKILL.md in skills/vdjdb-extract of antigenomics/vdjdb-db.
Open the folder on GitHubat commit 5dfc25f
Compare with similar skills
Vdjdb Extract 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 Extract this skillantigenomics/vdjdb-db | 157 | — | ~1.2k | Automated safety check: Pass | Custom licence | |
| Geo FetchClawBio/ClawBio | 1.2k | — | ~4.7k | Automated safety check: Pass | MIT | |
| Module Authoringdna-seq/just-dna-lite | 141 | — | ~4.8k | Automated safety check: Notes | AGPL-3.0 | |
| Bulkrna Cosinor RhythmTianGzlab/OmicsClaw | 161 | — | ~840 | Automated safety check: Pass | Apache-2.0 | |
| Nwb ConversionK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~1.9k | Automated safety check: Pass | MIT | |
| Auditing Part11 Trailsmaziyarpanahi/openmed | 5.5k | — | ~2.2k | Automated safety check: Pass | Apache-2.0 |
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Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.
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Generates and verifies 21 CFR Part 11-style audit trails — who/what/when, electronic signatures, and tamper-evidence — for OpenMed pipelines in GxP and clinical-trial (GCP) settings.
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A skill your agent uses when a tabular dataset (CSV, Excel, Parquet, Stata, SAS) needs a data dictionary.
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 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…
Vdjdb Structures
antigenomics/vdjdb-db
Extract and proofread deposited TCR-pMHC observations with the local tcren pipeline, then update the PDB aggregate chunk.
Related
Categories
Questions about Vdjdb Extract
What does Vdjdb Extract do?
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 Extract is an agent skill from 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 exports - into a VDJdb chunk TSV, verifying every extracted sequence, gene, allele and reference id back against the source.
When should I use Vdjdb Extract?
Vdjdb Extract fits situations like: submitter folder has to become a chunk file; before vdjdb-format and vdjdb-proofread.
How do I install Vdjdb Extract in Claude Code?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-extract -a claude-code`. Or copy the skill folder (skills/vdjdb-extract in antigenomics/vdjdb-db) into .claude/skills/vdjdb-extract in your project. Claude Code loads it when a task matches its description.
How do I install Vdjdb Extract in Codex?
Run `npx skills add antigenomics/vdjdb-db --skill vdjdb-extract -a codex`. Or copy the skill folder (skills/vdjdb-extract in antigenomics/vdjdb-db) into .agents/skills/vdjdb-extract in your project. Codex loads it when a task matches its description.
Can I use Vdjdb Extract 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-extract -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-extract, .gemini/skills/vdjdb-extract, .github/skills/vdjdb-extract and .opencode/skills/vdjdb-extract in your project.
What does Vdjdb Extract need to run?
SKILL.md names no scripts, command-line tools or credentials: Vdjdb Extract is instructions for the agent only.
Does Vdjdb Extract 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 Extract 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 Extract use?
Vdjdb Extract 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 Extract use?
About 1.2k tokens (SKILL.md is roughly 4.9k 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 Extract?
Skills that share tags, products or a category with Vdjdb Extract: Geo Fetch (ClawBio/ClawBio, 1.2k stars), Module Authoring (dna-seq/just-dna-lite, 141 stars), Bulkrna Cosinor Rhythm (TianGzlab/OmicsClaw, 161 stars) and Nwb Conversion (K-Dense-AI/scientific-agent-skills, 48k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Vdjdb Extract?
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.