jaspar-search

Retrieve transcription-factor binding profiles (PFMs/PWMs) from JASPAR, resolve gene symbols to JASPAR matrix IDs, and get TF metadata in multiple formats (MEME, TRANSFAC, PFM, JASPAR). Public API, no credential needed.

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Repository: eightmm/codex-science
Last source activity: July 10, 2026 at 15:27
Detected SKILL.md language: English
Stars: 2
Forks: 0

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quantitative-research

Execute auditable quantitative research across preregistered study design, statistical inference, numerical verification, dimensional analysis, uncertainty propagation, counterexample search, and formal proof. Use when a scientific or mathematical question needs actual computation and machine-readable evidence rather than only explanation.

2026-08-04

statistical-decision-analysis

Compare finite actions under uncertainty with explicit states, loss, utility or risk-neutral payoff, priors, experiment likelihoods, and a declared decision criterion. Use for Bayes risk, expected utility or payoff, pure-action minimax, minimax regret, dominance, posterior decision policies, EVPI/EVSI, experiment-cost decisions, and prior-threshold sensitivity; do not use for ordinary statistical testing, causal identification, strategic games, or MDP/POMDP/RL planning.

2026-08-04

cx-statistical-decision-analysis

2026-08-04

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name	jaspar-search
description	Retrieve transcription-factor binding profiles (PFMs/PWMs) from JASPAR, resolve gene symbols to JASPAR matrix IDs, and get TF metadata in multiple formats (MEME, TRANSFAC, PFM, JASPAR). Public API, no credential needed.
license	Apache-2.0

Jaspar Search (Codex-native)

Codex-native adaptation of Google DeepMind's jaspar-database skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

JASPAR API https://jaspar.elixir.no/api/v1/

Workflow

Resolve a TF symbol to a matrix id via /matrix/?search=<TF>, then fetch /matrix/<MA_ID>/ in the desired format.
Report the matrix id, TF name, collection, and version.

Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

Report the JASPAR release/collection (e.g. CORE) and matrix version.
Cite only matrix IDs actually returned.

jaspar-search

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More from this repository

More from this repository

Jaspar Search (Codex-native)

Gates (ask before proceeding)

Endpoints

Workflow

Boundaries

Jaspar Search (Codex-native)

Gates (ask before proceeding)

Endpoints

Workflow

Boundaries