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Agent skill

Enrichr API

by wentorai in wentorai/research-plugins

Perform gene set enrichment analysis using the Enrichr API. An agent skill from wentorai/research-plugins.

MITAuto-check passedMedia & Creative

Install Enrichr API

skills CLI
$ npx skills add wentorai/research-plugins --skill enrichr-api -a claude-code

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

GitHub CLI
$ gh skill install wentorai/research-plugins enrichr-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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/enrichr-api .claude/skills/enrichr-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/

Facts

Skill name
enrichr-api
GitHub stars
298
Used in
1 other repo
Token cost
~2k tokens
SKILL.md length
462 words
Files
1
Skills in repo
405
Repo updated
First seen
Licence
MIT

At a glance

Perform gene set enrichment analysis using the Enrichr API. An agent skill from wentorai/research-plugins.

  • Works in 2 steps: Submit Gene List → Retrieve Enrichment Results
  • Media & Creative work in your project
  • SKILL.md covers Overview, Two-Step Workflow, Core Endpoints and Available Libraries (225 Total), plus 4 more sections
  • Calls curl; reaches maayanlab.cloud

What it does

Enrichr API is an agent skill from wentorai/research-plugins. Perform gene set enrichment analysis using the Enrichr API

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 Media & Creative. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

  • Media & Creative work in your project

Example prompts

  • “/enrichr-api”

Requirements

  • Python 3

Workflow steps

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

  1. Submit Gene List
  2. Retrieve Enrichment Results

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. 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:

    • curl

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • maayanlab.cloud

    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

Enrichr API loads about 2k tokens when it runs. Until then it costs about 18 tokens; SKILL.md has 462 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~18
When it runs · the whole SKILL.md, loaded when a task matches
~2k

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

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 462 words, ~2,030 tokens.

Download SKILL.mdSave it as .claude/skills/enrichr-api/SKILL.md (or your agent's skills folder).
name
enrichr-api
description
Perform gene set enrichment analysis using the Enrichr API

Enrichr Gene Set Enrichment Analysis API

Overview

Enrichr is the most widely used gene set enrichment analysis tool, developed by the Ma'ayan Lab at the Icahn School of Medicine at Mount Sinai. It tests whether a user-supplied gene list is statistically over-represented in curated gene set libraries spanning pathways, ontologies, transcription factor targets, disease associations, and cell types. The API provides access to 225 background libraries covering over 500,000 annotated gene sets. Free, no authentication required.

Two-Step Workflow

Enrichr uses a submit-then-query pattern:

  1. POST gene list to /addList -- returns a userListId token
  2. GET enrichment from /enrich using that token and a chosen library

The userListId persists on the server, so you can run multiple library queries against the same submission without re-uploading.

Core Endpoints

Base URL
https://maayanlab.cloud/Enrichr
Step 1: Submit Gene List
bash
curl -X POST "https://maayanlab.cloud/Enrichr/addList" \
  -F "list=BRCA1
BRCA2
TP53
EGFR
MYC
PTEN
AKT1
KRAS
PIK3CA
RAF1" \
  -F "description=cancer_genes"

Response:

json
{
  "shortId": "8619200cc78f1513ff1029a04af90ad7",
  "userListId": 124544426
}

Genes are newline-separated. The request must use multipart/form-data (the -F flag), not application/x-www-form-urlencoded.

Step 2: Retrieve Enrichment Results
bash
curl "https://maayanlab.cloud/Enrichr/enrich?userListId=124544426&backgroundType=KEGG_2021_Human"

Response (first 3 of 143 results):

json
{
  "KEGG_2021_Human": [
    [1, "Breast cancer", 3.37e-22, 198530.0, 9815800.25,
     ["PIK3CA","MYC","PTEN","AKT1","KRAS","BRCA1","BRCA2","RAF1","TP53","EGFR"],
     4.82e-20, 0, 0],
    [2, "Endometrial cancer", 1.35e-19, 1595.2, 69306.12,
     ["PIK3CA","MYC","PTEN","AKT1","KRAS","RAF1","TP53","EGFR"],
     9.68e-18, 0, 0],
    [3, "Central carbon metabolism in cancer", 6.66e-19, 1285.68, 53809.88,
     ["PIK3CA","MYC","PTEN","AKT1","KRAS","RAF1","TP53","EGFR"],
     3.17e-17, 0, 0]
  ]
}

Each result array contains: [rank, term_name, p_value, z_score, combined_score, overlapping_genes, adjusted_p_value, old_p_value, old_adjusted_p_value].

View Submitted Gene List
bash
curl "https://maayanlab.cloud/Enrichr/view?userListId=124544426"
json
{
  "genes": ["PIK3CA","MYC","AKT1","PTEN","BRCA1","KRAS","BRCA2","EGFR","TP53","RAF1"],
  "description": "cancer_genes"
}
Export Results as TSV
bash
curl "https://maayanlab.cloud/Enrichr/export?userListId=124544426&backgroundType=KEGG_2021_Human&filename=results" \
  -o enrichr_results.txt
List Available Libraries
bash
curl "https://maayanlab.cloud/Enrichr/datasetStatistics"

Returns metadata for all 225 libraries, each entry containing libraryName, numTerms, geneCoverage, and genesPerTerm.

Available Libraries (225 Total)

Pathway Databases
LibraryTermsGenes
KEGG_20263528,110
KEGG_2021_Human3208,078
WikiPathways_2024_Human8298,281
Reactome_Pathways_20242,10511,671
BioCarta_20162371,348
Gene Ontology
LibraryTermsGenes
GO_Biological_Process_20255,34314,674
GO_Molecular_Function_20251,17411,484
GO_Cellular_Component_202546811,501
Disease and Phenotype
LibraryTermsGenes
DisGeNET9,82817,464
GWAS_Catalog_20252,36915,030
ClinVar_20256093,481
OMIM_Disease901,759
Human_Phenotype_Ontology1,7793,096
Transcription Factor and Epigenomics
LibraryTermsGenes
ChEA_202275718,365
ENCODE_TF_ChIP-seq_201581626,382
JASPAR_PWM_Human_202567518,518
Show full SKILL.md (191 more words)Show less
Cell Type and Tissue
LibraryTermsGenes
CellMarker_20241,69212,642
ARCHS4_Tissues10821,809
Human_Gene_Atlas8413,373
Cancer and Drug
LibraryTermsGenes
MSigDB_Hallmark_2020504,383
MSigDB_Oncogenic_Signatures18911,250
DGIdb_Drug_Targets_20246592,513

Rate Limits

  • No authentication or API key required
  • No officially published rate limits, but automated queries should include reasonable delays (1-2 seconds between requests)
  • Very large gene lists (>3,000 genes) may time out on some libraries
  • The userListId persists server-side; avoid re-submitting the same list repeatedly

Academic Use Cases

  • Differential expression follow-up: Submit DEGs from RNA-seq to identify enriched pathways and GO terms
  • GWAS hit annotation: Map GWAS-significant genes to disease phenotypes via DisGeNET or GWAS_Catalog
  • Drug target discovery: Cross-reference gene signatures against DGIdb_Drug_Targets for druggable candidates
  • Transcription factor analysis: Identify upstream regulators via ChEA or ENCODE TF libraries

Python Usage

python
import requests

ENRICHR_URL = "https://maayanlab.cloud/Enrichr"


def submit_gene_list(genes: list[str], description: str = "") -> int:
    """Submit a gene list to Enrichr, return userListId."""
    payload = {
        "list": (None, "\n".join(genes)),
        "description": (None, description),
    }
    resp = requests.post(f"{ENRICHR_URL}/addList", files=payload)
    resp.raise_for_status()
    return resp.json()["userListId"]


def get_enrichment(user_list_id: int, library: str) -> list[dict]:
    """Retrieve enrichment results for a given library."""
    resp = requests.get(
        f"{ENRICHR_URL}/enrich",
        params={"userListId": user_list_id, "backgroundType": library},
    )
    resp.raise_for_status()
    data = resp.json()

    results = []
    for entry in data.get(library, []):
        results.append({
            "rank": entry[0],
            "term": entry[1],
            "p_value": entry[2],
            "z_score": entry[3],
            "combined_score": entry[4],
            "genes": entry[5],
            "adj_p_value": entry[6],
        })
    return results


def get_libraries() -> list[dict]:
    """List all available Enrichr libraries."""
    resp = requests.get(f"{ENRICHR_URL}/datasetStatistics")
    resp.raise_for_status()
    return resp.json()["statistics"]


# Example: enrichment analysis of cancer-related genes
genes = ["BRCA1", "BRCA2", "TP53", "EGFR", "MYC",
         "PTEN", "AKT1", "KRAS", "PIK3CA", "RAF1"]

list_id = submit_gene_list(genes, "cancer_genes")
print(f"Submitted gene list, ID: {list_id}")

# Query KEGG pathways
kegg = get_enrichment(list_id, "KEGG_2021_Human")
print(f"\nTop 5 KEGG pathways ({len(kegg)} total):")
for r in kegg[:5]:
    print(f"  {r['rank']}. {r['term']}")
    print(f"     p={r['p_value']:.2e}, adj_p={r['adj_p_value']:.2e}, "
          f"genes={','.join(r['genes'][:5])}...")

# Query GO Biological Process
go_bp = get_enrichment(list_id, "GO_Biological_Process_2023")
print(f"\nTop 5 GO Biological Processes ({len(go_bp)} total):")
for r in go_bp[:5]:
    print(f"  {r['rank']}. {r['term']}")
    print(f"     p={r['p_value']:.2e}, genes={','.join(r['genes'])}")

References

  • Enrichr Web App
  • Enrichr API Docs
  • Chen, E.Y. et al. (2013). "Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool." BMC Bioinformatics 14:128.
  • Kuleshov, M.V. et al. (2016). "Enrichr: a comprehensive gene set enrichment analysis web server 2016 update." Nucleic Acids Res. 44(W1).
  • Xie, Z. et al. (2021). "Gene Set Knowledge Discovery with Enrichr." Current Protocols 1(3):e90.

© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/domains/biomedical/enrichr-api of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

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Categories

Questions about Enrichr API

What does Enrichr API do?

Perform gene set enrichment analysis using the Enrichr API. An agent skill from wentorai/research-plugins. Enrichr API is an agent skill from wentorai/research-plugins.

When should I use Enrichr API?

Enrichr API fits situations like: media & Creative work in your project.

How do I install Enrichr API in Claude Code?

Run `npx skills add wentorai/research-plugins --skill enrichr-api -a claude-code`. Or copy the skill folder (skills/domains/biomedical/enrichr-api in wentorai/research-plugins) into .claude/skills/enrichr-api in your project. Claude Code loads it when a task matches its description.

How do I install Enrichr API in Codex?

Run `npx skills add wentorai/research-plugins --skill enrichr-api -a codex`. Or copy the skill folder (skills/domains/biomedical/enrichr-api in wentorai/research-plugins) into .agents/skills/enrichr-api in your project. Codex loads it when a task matches its description.

Can I use Enrichr 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 wentorai/research-plugins --skill enrichr-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/enrichr-api, .gemini/skills/enrichr-api, .github/skills/enrichr-api and .opencode/skills/enrichr-api in your project.

What does Enrichr API need to run?

Going by SKILL.md and its folder, Enrichr API needs the command-line tools its instructions call (curl). Our summary lists: Python 3.

Does Enrichr API access the network?

SKILL.md names 1 domain. In commands or code: maayanlab.cloud; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Enrichr 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. Review the folder before installing.

What licence does Enrichr API use?

Enrichr API is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Enrichr API use?

About 2k tokens (SKILL.md is roughly 8.1k 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 Enrichr API?

Skills that share tags, products or a category with Enrichr API: Guizang Social Cards (op7418/guizang-social-card-skill, 7.4k stars), Weekly Changelog Video (heygen-com/hyperframes, 59k stars), Anthropic Brand Styling (anthropics/skills, 180k stars) and MoneyPrinterTurbo Video Generator (harry0703/MoneyPrinterTurbo, 129k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Enrichr API?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.

Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.