Agent skill

Jaspar API

by aipoch in aipoch/medical-research-skills

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API.

Install Jaspar API

skills CLI

$ npx skills add aipoch/medical-research-skills --skill jaspar-api -a claude-code

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills jaspar-api --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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .claude/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .claude/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api

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 aipoch/medical-research-skills --skill jaspar-api -a codex

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills jaspar-api --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .agents/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .agents/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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 aipoch/medical-research-skills --skill jaspar-api -a cursor

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills jaspar-api --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .cursor/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .cursor/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/jaspar-api'

--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 aipoch/medical-research-skills --skill jaspar-api -a gemini-cli

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills jaspar-api --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/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .gemini/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .gemini/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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 aipoch/medical-research-skills jaspar-api

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 aipoch/medical-research-skills --skill jaspar-api -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .github/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .github/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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 aipoch/medical-research-skills --skill jaspar-api -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 aipoch/medical-research-skills jaspar-api --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/jaspar-api' .opencode/skills/jaspar-api && 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 "jaspar-api" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/jaspar-api into .opencode/skills/jaspar-api/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "jaspar-api", 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: jaspar-api
GitHub stars: 2k
Token cost: ~1.1k tokens
SKILL.md length: 441 words
Files: 4 (incl. scripts, references)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API.

Works in 4 steps: Search Matrices (Profiles) → Get Matrix Details → Infer Profile from Sequence → …
User wants to search for transcription factors
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 3 more sections
Runs Python scripts from its folder; calls python

What it does

Jaspar API is an agent skill from aipoch/medical-research-skills. Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files, including scripts and reference files (for example `jaspar-api_audit_result_v1.json`, `references/api_docs.md` and `scripts/jaspar_client.py`).

It sits in Media & Creative, covering Transcription and REST APIs. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

User wants to search for transcription factors
Retrieve matrix details (PFM/PWM)
Infer profiles from protein sequences
Explore JASPAR collections

Example prompts

“/jaspar-api”

Requirements

Python 3

Workflow steps

4 steps, taken from the step headings in SKILL.md.

Search Matrices (Profiles)
Get Matrix Details
Infer Profile from Sequence
Collections and Species

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. 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
Ships 1 file in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- jaspar.elixir.no
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

Jaspar API loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 72 tokens; SKILL.md has 441 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~72
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~1.6k

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); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 441 words, ~1,100 tokens.

Download SKILL.mdSave it as .claude/skills/jaspar-api/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.

name: jaspar-api
description: Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.
license: MIT
author: AIPOCH

Source: https://github.com/aipoch/medical-research-skills

JASPAR API

This skill provides access to the JASPAR database (https://jaspar.elixir.no/).

When to Use

Use this skill when you need access jaspar database for transcription factor binding profiles (matrices), collections, and species via rest api. use when user wants to search for transcription factors, retrieve matrix details (pfm/pwm), infer profiles from protein sequences, or explore jaspar collections in a reproducible workflow.
Use this skill when a evidence insight task needs a packaged method instead of ad-hoc freeform output.
Use this skill when the user expects a concrete deliverable, validation step, or file-based result.
Use this skill when scripts/jaspar_client.py is the most direct path to complete the request.
Use this skill when you need the jaspar-api package behavior rather than a generic answer.

Key Features

Scope-focused workflow aligned to: Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Use when user wants to search for transcription factors, retrieve matrix details (PFM/PWM), infer profiles from protein sequences, or explore JASPAR collections.
Packaged executable path(s): scripts/jaspar_client.py.
Reference material available in references/ for task-specific guidance.
Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

Python: 3.10+. Repository baseline for current packaged skills.
Third-party packages: not explicitly version-pinned in this skill package. Add pinned versions if this skill needs stricter environment control.

Example Usage

See ## Usage above for related details.

bash

cd "20260316/scientific-skills/Evidence Insight/jaspar-api"
python -m py_compile scripts/jaspar_client.py
python scripts/jaspar_client.py --help

Example run plan:

Confirm the user input, output path, and any required config values.
Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
Run python scripts/jaspar_client.py with the validated inputs.
Review the generated output and return the final artifact with any assumptions called out.

Show full SKILL.md (163 more words)Show less

Implementation Details

Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
Primary implementation surface: scripts/jaspar_client.py.
Reference guidance: references/ contains supporting rules, prompts, or checklists.
Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Usage

1. Search Matrices (Profiles)

Search for transcription factor binding profiles.

bash

python scripts/jaspar_client.py matrix_list --search "SMAD3" --tax_group "Vertebrates"

Supported parameters:

--search: Search term
--collection: e.g., CORE, CNE
--tax_group: e.g., Vertebrates, Plants
--tax_id: e.g., 9606 (Human)
--tf_class: Transcription factor class
--version: latest (default) or specific
--page_size: Results per page

2. Get Matrix Details

Retrieve details for a specific matrix ID (e.g., MA0001.1).

bash

python scripts/jaspar_client.py matrix_read MA0001.1

3. Infer Profile from Sequence

Infer matrix profiles given a protein sequence.

bash

python scripts/jaspar_client.py infer "SEQUENCE_STRING"

4. Collections and Species

List collections:

bash

python scripts/jaspar_client.py collections_list

Get details for a species (by tax_id):

bash

python scripts/jaspar_client.py species_read 9606

References

See references/api_docs.md for full parameter lists and endpoint details.

Files

SKILL.md and 3 other files (scripts, references) in scientific-skills/Evidence Insight/jaspar-api of aipoch/medical-research-skills.

SKILL.md
jaspar-api_audit_result_v1.json
references/api_docs.md
scripts/jaspar_client.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Jaspar API 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.

Jaspar API compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Jaspar API this skillaipoch/medical-research-skills	2k	—	~1.1k	Automated safety check: Pass	MIT	21 days ago
Azure Speech To Text REST Pymicrosoft/skills	3.1k	6 repos	~3k	Automated safety check: Pass	MIT	2 days ago
Vbook ExtensionsDarkrai9x/vbook-extensions	108	—	~4.9k	Automated safety check: Pass	None	today
Video Dataoxylabs/agent-skills	875	—	~1.4k	Automated safety check: Pass	MIT	8 days ago
Telnyx Voice Streaming Curlteam-telnyx/ai	220	—	~3.4k	Automated safety check: Pass	MIT	3 days ago
Native Subtitle Quote Imagechengyi-ai/native-subtitle-quote-image	2.2k	2 repos	~1.8k	Automated safety check: Pass	MIT	yesterday

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Questions about Jaspar API

What does Jaspar API do?

Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API. Jaspar API is an agent skill from aipoch/medical-research-skills. Access JASPAR database for transcription factor binding profiles (matrices), collections, and species via REST API.

When should I use Jaspar API?

Jaspar API fits situations like: user wants to search for transcription factors; retrieve matrix details (PFM/PWM); infer profiles from protein sequences; explore JASPAR collections.

How do I install Jaspar API in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill jaspar-api -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/jaspar-api in aipoch/medical-research-skills) into .claude/skills/jaspar-api in your project. Claude Code loads it when a task matches its description.

How do I install Jaspar API in Codex?

Run `npx skills add aipoch/medical-research-skills --skill jaspar-api -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/jaspar-api in aipoch/medical-research-skills) into .agents/skills/jaspar-api in your project. Codex loads it when a task matches its description.

Can I use Jaspar API 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 aipoch/medical-research-skills --skill jaspar-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/jaspar-api, .gemini/skills/jaspar-api, .github/skills/jaspar-api and .opencode/skills/jaspar-api in your project.

What does Jaspar API need to run?

Going by SKILL.md and its folder, Jaspar API needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Jaspar API access the network?

SKILL.md names 1 domain. As links in the text: jaspar.elixir.no. This is read from the text; nothing was executed.

Is Jaspar API 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Jaspar API use?

Jaspar API is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Jaspar API use?

About 1.1k tokens (SKILL.md is roughly 4.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 516 tokens, read only when the agent opens those files.

What are the alternatives to Jaspar API?

Skills that share tags, products or a category with Jaspar API: Azure Speech To Text REST Py (microsoft/skills, 3.1k stars), Vbook Extensions (Darkrai9x/vbook-extensions, 108 stars), Video Data (oxylabs/agent-skills, 875 stars) and Telnyx Voice Streaming Curl (team-telnyx/ai, 220 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Jaspar API?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-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.

Install Jaspar API

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

JASPAR API

When to Use

Key Features

Dependencies

Example Usage

Implementation Details

Usage

1. Search Matrices (Profiles)

2. Get Matrix Details

3. Infer Profile from Sequence

4. Collections and Species

References

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about Jaspar API