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gget · FreedomIntelligence | DecimalAI

Scienceby FreedomIntelligence

gget

CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bioservices.

Never made a case worse

SkillScore

SkillScore87/100

Test results 87

Safety

3/3 safety checks passed

Code scan
Intent
Content

What it changes

0%87%of test cases passed +87 pts

Without skill0 of 23

With skill20 of 23

20 fixed0 passed either way3 still failing0 broke

Measured on gemini-3.6-flash7/26/2026v1

Track record

Agent runs: 0; All time

Use this skill

Your agent runs on

Adds every file the skill has, pinned so you can update it. No account needed.

pip install "decimalai>=0.15"
decimalai skills add gget
claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"

The same install from Python, for a notebook or a setup script.

Install

pip install "decimalai>=0.15"

Add the skill

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

print("Added. Start Claude Code with the command below.")

Start Claude Code with it

claude --plugin-dir "$(git rev-parse --show-toplevel 2>/dev/null || pwd)/.agents"

Type these in a Claude Code session. No account or API key. It writes the skill and any files it bundles, and asks first when its safety rating isn't Passed.

Add the DecimalAI plugin, once

/plugin marketplace add decimal-labs/decimalai-claude-plugins
/plugin install decimalai@decimalai

Install this skill

/decimalai:install gget

The plugin needs python3 and curl on your machine.

No Python or account. Claude Code picks it up in its next session.

Save it into your project

curl -fsSL --create-dirs -o .claude/skills/gget/SKILL.md https://app.decimal.ai/s/gget/SKILL.md

Copy SKILL.md

Save it in your project, as

.claude/skills/gget/SKILL.md

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Claude Code docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[claude-agent-sdk]"
decimalai skills add gget

Add it to your agent

import asyncio

from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

async def main():
    question = "Hello!"
    async with support.run(question) as run:  # one user message, one run
        async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
            print(message)

# In a notebook or async code: await main()
asyncio.run(main())

Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

The same install from Python, for a notebook or a setup script. agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[claude-agent-sdk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import asyncio

from claude_agent_sdk import ClaudeAgentOptions
from decimalai.claude_agent_sdk import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

async def main():
    question = "Hello!"
    async with support.run(question) as run:  # one user message, one run
        async for message in run.query(options=ClaudeAgentOptions(max_turns=6)):
            print(message)

# In a notebook or async code: await main()
asyncio.run(main())

Prefer its own loader? ClaudeAgentOptions(plugins=[skills_plugin()], skills="all") reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from claude_agent_sdk import ClaudeAgentOptions, query

skill = Path(".agents/skills/gget/SKILL.md").read_text()
options = ClaudeAgentOptions(system_prompt=f"You are a helpful agent.\n\n{skill}", max_turns=6)

async def main():
    async for message in query(prompt="Hello!", options=options):
        print(message)

# In a notebook or async code: await main()
asyncio.run(main())

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Claude Agent SDK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[openai-agents]"
decimalai skills add gget

Add it to your agent

from agents import Agent, Runner
from decimalai.openai_agents import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    name=support.name,
    instructions=support.instructions,  # your prompt, then the skill list
    tools=[*support.tools],             # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.

Install

pip install "decimalai[openai-agents]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from agents import Agent, Runner
from decimalai.openai_agents import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    name=support.name,
    instructions=support.instructions,  # your prompt, then the skill list
    tools=[*support.tools],             # your tools, then load_skill
)
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

Using SandboxAgent? capabilities=[Shell(), decimalai.openai_agents.sandbox_skills()] points its own loader at the same folder.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from agents import Agent, Runner

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = Agent(name="support", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await Runner.run(agent, "Hello!")
result = Runner.run_sync(agent, "Hello!")

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

OpenAI Agents docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[openai]"
decimalai skills add gget

Add it to your agent

import json

from openai import OpenAI
from decimalai.openai import agent_config

client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
                   "required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    # run.system is your prompt, then the skill list.
    messages = [{"role": "system", "content": run.system}, run.message]
    while True:
        reply = client.chat.completions.create(
            model="gpt-5.4-mini",
            messages=messages,
            tools=[*TOOLS, *run.tools],  # your tools, then load_skill
        ).choices[0].message
        messages.append(reply)
        if not reply.tool_calls:
            break
        for call in reply.tool_calls:
            # load_skill is answered by the run; your own tools by FUNCTIONS.
            function = FUNCTIONS.get(call.function.name)
            messages.append(run.tool_result(call) or {
                "role": "tool", "tool_call_id": call.id,
                "content": function(**json.loads(call.function.arguments)) if function
                else f"There is no tool named {call.function.name!r}.",
            })
print(reply.content)

# The Responses API takes run.response_tools instead of run.tools.

Install

pip install "decimalai[openai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import json

from openai import OpenAI
from decimalai.openai import agent_config

client = OpenAI()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your tools, as Chat Completions takes them, and what answers each.
TOOLS = [{"type": "function", "function": {
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters": {"type": "object", "properties": {"order_id": {"type": "string"}},
                   "required": ["order_id"]},
}}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    # run.system is your prompt, then the skill list.
    messages = [{"role": "system", "content": run.system}, run.message]
    while True:
        reply = client.chat.completions.create(
            model="gpt-5.4-mini",
            messages=messages,
            tools=[*TOOLS, *run.tools],  # your tools, then load_skill
        ).choices[0].message
        messages.append(reply)
        if not reply.tool_calls:
            break
        for call in reply.tool_calls:
            # load_skill is answered by the run; your own tools by FUNCTIONS.
            function = FUNCTIONS.get(call.function.name)
            messages.append(run.tool_result(call) or {
                "role": "tool", "tool_call_id": call.id,
                "content": function(**json.loads(call.function.arguments)) if function
                else f"There is no tool named {call.function.name!r}.",
            })
print(reply.content)

# The Responses API takes run.response_tools instead of run.tools.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from openai import OpenAI

client = OpenAI()
skill = Path(".agents/skills/gget/SKILL.md").read_text()
reply = client.chat.completions.create(
    model="gpt-5.4-mini",
    messages=[
        {"role": "system", "content": f"You are a helpful agent.\n\n{skill}"},
        {"role": "user", "content": "Hello!"},
    ],
).choices[0].message

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

OpenAI SDK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[anthropic]"
decimalai skills add gget

Add it to your agent

import anthropic
from decimalai.anthropic import agent_config

client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

question = "Hello!"
with support.run(question) as run:  # one user message, one run
    answer = client.beta.messages.tool_runner(
        model="claude-haiku-5-5",
        max_tokens=4096,
        system=run.system,     # your prompt, then the skill list
        tools=[*run.tools],    # your tools, then load_skill
        messages=[{"role": "user", "content": question}],
    ).until_done()

Install

pip install "decimalai[anthropic]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import anthropic
from decimalai.anthropic import agent_config

client = anthropic.Anthropic()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

question = "Hello!"
with support.run(question) as run:  # one user message, one run
    answer = client.beta.messages.tool_runner(
        model="claude-haiku-5-5",
        max_tokens=4096,
        system=run.system,     # your prompt, then the skill list
        tools=[*run.tools],    # your tools, then load_skill
        messages=[{"role": "user", "content": question}],
    ).until_done()

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
import anthropic

client = anthropic.Anthropic()
skill = Path(".agents/skills/gget/SKILL.md").read_text()
reply = client.messages.create(
    model="claude-haiku-5-5",
    max_tokens=4096,
    system=f"You are a helpful agent.\n\n{skill}",
    messages=[{"role": "user", "content": "Hello!"}],
)

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Anthropic docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[google-genai]"
decimalai skills add gget

Add it to your agent

from google import genai
from google.genai import types
from decimalai.google_genai import agent_config

client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
                               "required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    config = types.GenerateContentConfig(
        system_instruction=run.system,     # your prompt, then the skill list
        tools=[*TOOLS, *run.tool_params],  # your functions, then load_skill
    )
    contents = [{"role": "user", "parts": [{"text": run.message}]}]
    while True:
        response = client.models.generate_content(
            model="gemini-3.5-flash", contents=contents, config=config,
        )
        if not response.function_calls:
            break
        contents.append(response.candidates[0].content)
        parts = []
        for call in response.function_calls:
            # load_skill is answered by the run; your own functions by FUNCTIONS.
            # A loop of your own rather than automatic function calling, which
            # raises KeyError when the model asks for a function you did not pass.
            function = FUNCTIONS.get(call.name)
            parts.append(run.tool_result(call) or {"function_response": {
                "name": call.name, "id": call.id,
                "response": {"result": function(**(call.args or {})) if function
                             else f"There is no function named {call.name!r}."},
            }})
        contents.append({"role": "user", "parts": parts})
print(response.text)

Install

pip install "decimalai[google-genai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from google import genai
from google.genai import types
from decimalai.google_genai import agent_config

client = genai.Client()
# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")


def lookup_order(order_id: str) -> str:
    return f"Order {order_id} shipped yesterday."


# Your functions, as declarations for the model, and what answers each.
TOOLS = [{"function_declarations": [{
    "name": "lookup_order",
    "description": "Look up the status of an order.",
    "parameters_json_schema": {"type": "object", "properties": {"order_id": {"type": "string"}},
                               "required": ["order_id"]},
}]}]
FUNCTIONS = {"lookup_order": lookup_order}

question = "Where is order A1001?"
with support.run(question) as run:  # one user message, one run
    config = types.GenerateContentConfig(
        system_instruction=run.system,     # your prompt, then the skill list
        tools=[*TOOLS, *run.tool_params],  # your functions, then load_skill
    )
    contents = [{"role": "user", "parts": [{"text": run.message}]}]
    while True:
        response = client.models.generate_content(
            model="gemini-3.5-flash", contents=contents, config=config,
        )
        if not response.function_calls:
            break
        contents.append(response.candidates[0].content)
        parts = []
        for call in response.function_calls:
            # load_skill is answered by the run; your own functions by FUNCTIONS.
            # A loop of your own rather than automatic function calling, which
            # raises KeyError when the model asks for a function you did not pass.
            function = FUNCTIONS.get(call.name)
            parts.append(run.tool_result(call) or {"function_response": {
                "name": call.name, "id": call.id,
                "response": {"result": function(**(call.args or {})) if function
                             else f"There is no function named {call.name!r}."},
            }})
        contents.append({"role": "user", "parts": parts})
print(response.text)

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from google import genai
from google.genai import types

client = genai.Client()
skill = Path(".agents/skills/gget/SKILL.md").read_text()
response = client.models.generate_content(
    model="gemini-3.5-flash",
    contents="Hello!",
    config=types.GenerateContentConfig(system_instruction=f"You are a helpful agent.\n\n{skill}"),
)

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Gemini API docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[langchain]" langchain-openai
decimalai skills add gget

Add it to your agent

from langchain.agents import create_agent
from decimalai.langchain import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = create_agent(
    "openai:gpt-5.4-mini",
    tools=[],                         # your tools; the middleware adds load_skill
    middleware=[support.middleware],  # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

Install

pip install "decimalai[langchain]" langchain-openai

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from langchain.agents import create_agent
from decimalai.langchain import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = create_agent(
    "openai:gpt-5.4-mini",
    tools=[],                         # your tools; the middleware adds load_skill
    middleware=[support.middleware],  # your prompt, the skill list and load_skill
)
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from langchain.agents import create_agent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = create_agent("openai:gpt-5.4-mini", tools=[], system_prompt=f"You are a helpful agent.\n\n{skill}")
result = agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

LangChain docs

CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"
decimalai skills add gget

Add it to your agent

import decimalai.crewai
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                               # your own CrewAI LLM
    skills=decimalai.crewai.skills(),      # the installed folder
    tools=decimalai.crewai.skill_tools(),  # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

The same install from Python, for a notebook or a setup script. CrewAI's own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" "crewai>=1.15.27"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import decimalai.crewai
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                               # your own CrewAI LLM
    skills=decimalai.crewai.skills(),      # the installed folder
    tools=decimalai.crewai.skill_tools(),  # reads a skill's files, runs its scripts
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

No DecimalAI package. CrewAI's own loader reads the folder, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from crewai import Agent, Crew, Task

agent = Agent(
    role="Support", goal="Help the customer", backstory="A support agent.",
    llm=llm,                         # your own CrewAI LLM
    skills=[Path(".agents/skills")],
)
task = Task(description="Hello!", expected_output="an answer", agent=agent)
Crew(agents=[agent], tasks=[task]).kickoff()

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

CrewAI docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[adk]"
decimalai skills add gget

Add it to your agent

from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = LlmAgent(
    name="support",          # ADK needs a Python identifier
    model="gemini-3.5-flash",
    instruction=support.instruction,  # your prompt, then the skill list
    tools=[*support.tools],           # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])

Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

Install

pip install "decimalai[adk]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from decimalai.adk import DecimalAIPlugin, agent_config
from google.adk.agents import LlmAgent
from google.adk.apps import App

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = LlmAgent(
    name="support",          # ADK needs a Python identifier
    model="gemini-3.5-flash",
    instruction=support.instruction,  # your prompt, then the skill list
    tools=[*support.tools],           # your tools, then load_skill
)
# DecimalAIPlugin makes each invocation of runners built from this App one trace.
app = App(name="support", root_agent=agent, plugins=[DecimalAIPlugin()])

Prefer ADK's own loader? SkillToolset(skills=decimalai.adk.skills(), ...) reads the same folder. Use one or the other: a skill delivered both ways reaches the prompt twice.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from google.adk.agents import LlmAgent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = LlmAgent(
    name="support",
    model="gemini-3.5-flash",
    instruction=lambda context: f"You are a helpful agent.\n\n{skill}",
)

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Google ADK docs

agent_config() hands your agent the skill. With no DecimalAI key it reads your project's files and sends nothing. Needs SDK 0.27 or newer.

Install

pip install "decimalai[pydantic-ai]"
decimalai skills add gget

Add it to your agent

from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    "openai:gpt-4o-mini",
    name=support.name,
    tools=[],                 # your tools; the capability adds load_skill
    capabilities=[support],   # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.

Install

pip install "decimalai[pydantic-ai]"

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from pydantic_ai import Agent
from decimalai.pydantic_ai import agent_config

# With no DECIMAL_API_KEY this reads the skills your project lists, from disk.
support = agent_config("support", fallback="You are a helpful agent.")

agent = Agent(
    "openai:gpt-4o-mini",
    name=support.name,
    tools=[],                 # your tools; the capability adds load_skill
    capabilities=[support],   # your prompt, the skill list and load_skill
)
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

On the Pydantic AI harness, decimalai.pydantic_ai_harness.skills(project) uses its own loader instead.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from pydantic_ai import Agent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = Agent("openai:gpt-4o-mini", instructions=f"You are a helpful agent.\n\n{skill}")
# In a notebook or async code: result = await agent.run("Hello!")
result = agent.run_sync("Hello!")

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Pydantic AI docs

Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" deepagents
decimalai skills add gget

Add it to your agent

import decimalai.deepagents
from deepagents import create_deep_agent

agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).

The same install from Python, for a notebook or a setup script. Deep Agents' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" deepagents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import decimalai.deepagents
from deepagents import create_deep_agent

agent = create_deep_agent(model=model, **decimalai.deepagents.skills())
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

The default backend reads files but has no shell. To run a skill's scripts, pass skills(backend=LocalShellBackend(...)).

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from deepagents import create_deep_agent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = create_deep_agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent.invoke({"messages": [{"role": "user", "content": "Hello!"}]})

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Deep Agents docs

Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework
decimalai skills add gget

Add it to your agent

import asyncio

from agent_framework import Agent
from decimalai.agent_framework import skills

agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))

It caches skills by default, so restart the process after decimalai skills update.

The same install from Python, for a notebook or a setup script. Its own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" agent-framework

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

import asyncio

from agent_framework import Agent
from decimalai.agent_framework import skills

agent = Agent(client=client, instructions="You are a helpful agent.", context_providers=[skills()])
asyncio.run(agent.run("Hello!"))

It caches skills by default, so restart the process after decimalai skills update.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

import asyncio
from pathlib import Path
from agent_framework import Agent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = Agent(client=client, instructions=f"You are a helpful agent.\n\n{skill}")
asyncio.run(agent.run("Hello!"))

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Microsoft Agent Framework docs

Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents
decimalai skills add gget

Add it to your agent

from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell

agent = Agent(
    model=model,                # always pass one: the default is Amazon Bedrock
    system_prompt="You are a helpful agent.",
    tools=[file_editor, shell],
    plugins=[skills()],
)
agent("Hello!")

Strands loads an agent's skills once, so build the agent again after decimalai skills update.

The same install from Python, for a notebook or a setup script. Strands' own skill loader reads the installed folder. No DecimalAI account needed.

Install

pip install "decimalai>=0.16" strands-agents

Add it to your agent

from decimalai import skillpkg

# Writes .agents/skills and .decimal/skills.toml. Safe to run twice.
result = skillpkg.add("gget")
if result.exit_code:
    raise SystemExit(result.problems)

from decimalai.strands import skills
from strands import Agent
from strands.vended_tools import file_editor, shell

agent = Agent(
    model=model,                # always pass one: the default is Amazon Bedrock
    system_prompt="You are a helpful agent.",
    tools=[file_editor, shell],
    plugins=[skills()],
)
agent("Hello!")

Strands loads an agent's skills once, so build the agent again after decimalai skills update.

No DecimalAI package. The whole skill goes in every prompt, and nothing pins or updates it.

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

Give it to your agent

from pathlib import Path
from strands import Agent

skill = Path(".agents/skills/gget/SKILL.md").read_text()
agent = Agent(model=model, system_prompt=f"You are a helpful agent.\n\n{skill}")
agent("Hello!")

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Strands docs

Adds every file the skill has, pinned so you can update it. Cursor, Copilot, Cline and Warp read this folder by themselves.

pip install "decimalai>=0.15"
decimalai skills add gget

No Python or account. Cursor, Copilot, Cline and Warp read this folder by themselves.

Save it into your project

curl -fsSL --create-dirs -o .agents/skills/gget/SKILL.md https://app.decimal.ai/s/gget/SKILL.md

Copy SKILL.md

Save it in your project, as

.agents/skills/gget/SKILL.md

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Cursor and other editors docs

Fetch the file and give its text to your model as instructions. No account or package needed.

Get the file

curl -fsSL https://app.decimal.ai/s/gget/SKILL.md

Read the summary as JSON

curl -fsSL https://app.decimal.ai/s/gget.json

This gets SKILL.md only. The skill's 6 other files are not included.

Other ways to add it

Other setups docs

You don't need a DecimalAI account.

Version: v1, tested 7/26/2026
Source: FreedomIntelligence/OpenClaw-Medical-Skills ↗
License: Not recorded

Manage it in DecimalAI

Saved prompts and skills, pinned versions, and traces of this skill in your runs. DecimalAI does not run your agent.

Claude Code reads files from your project, so DecimalAI config does not apply there.

On Claude Agent SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On OpenAI Agents: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On OpenAI SDK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Anthropic: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Gemini API: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On LangChain: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On CrewAI: set DECIMAL_API_KEY and add decimalai.init(crewai=True) to record runs and skill use. The skill version stays in your repo.

On Google ADK: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Pydantic AI: save the skill to an agent here, set DECIMAL_API_KEY, and the same code uses it with no command to run. Changes you save reach the next run with no redeploy.

On Deep Agents: set DECIMAL_API_KEY and add decimalai.init(langchain=True) to record runs and skill use. The skill version stays in your repo.

On Microsoft Agent Framework: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.

On Strands: set DECIMAL_API_KEY and add decimalai.init(otel=True, agent_name="support") to record runs and skill use. The skill version stays in your repo.

Editors read files from your project, so DecimalAI config does not apply there.

Anywhere else: record a use with decimalai.log_skill_activation() inside a trace.

Use this skill

SKILL.md

gget

Overview

gget is a command-line bioinformatics tool and Python package providing unified access to 20+ genomic databases and analysis methods. Query gene information, sequence analysis, protein structures, expression data, and disease associations through a consistent interface. All gget modules work both as command-line tools and as Python functions.

Important: The databases queried by gget are continuously updated, which sometimes changes their structure. gget modules are tested automatically on a biweekly basis and updated to match new database structures when necessary.

Installation

Install gget in a clean virtual environment to avoid conflicts:

# Using uv (recommended)
uv uv pip install gget

# Or using pip
uv pip install --upgrade gget

# In Python/Jupyter
import gget

Quick Start

Basic usage pattern for all modules:

# Command-line
gget <module> [arguments] [options]

# Python
gget.module(arguments, options)

Most modules return:

Command-line: JSON (default) or CSV with -csv flag
Python: DataFrame or dictionary

Common flags across modules:

-o/--out: Save results to file
-q/--quiet: Suppress progress information
-csv: Return CSV format (command-line only)

Module Categories

1. Reference & Gene Information

gget ref - Reference Genome Downloads

Retrieve download links and metadata for Ensembl reference genomes.

Parameters:

species: Genus_species format (e.g., 'homo_sapiens', 'mus_musculus'). Shortcuts: 'human', 'mouse'
-w/--which: Specify return types (gtf, cdna, dna, cds, cdrna, pep). Default: all
-r/--release: Ensembl release number (default: latest)
-l/--list_species: List available vertebrate species
-liv/--list_iv_species: List available invertebrate species
-ftp: Return only FTP links
-d/--download: Download files (requires curl)

Examples:

# List available species
gget ref --list_species

# Get all reference files for human
gget ref homo_sapiens

# Download only GTF annotation for mouse
gget ref -w gtf -d mouse

# Python
gget.ref("homo_sapiens")
gget.ref("mus_musculus", which="gtf", download=True)

gget search - Gene Search

Locate genes by name or description across species.

Parameters:

searchwords: One or more search terms (case-insensitive)
-s/--species: Target species (e.g., 'homo_sapiens', 'mouse')
-r/--release: Ensembl release number
-t/--id_type: Return 'gene' (default) or 'transcript'
-ao/--andor: 'or' (default) finds ANY searchword; 'and' requires ALL
-l/--limit: Maximum results to return

Returns: ensembl_id, gene_name, ensembl_description, ext_ref_description, biotype, URL

Examples:

# Search for GABA-related genes in human
gget search -s human gaba gamma-aminobutyric

# Find specific gene, require all terms
gget search -s mouse -ao and pax7 transcription

# Python
gget.search(["gaba", "gamma-aminobutyric"], species="homo_sapiens")

gget info - Gene/Transcript Information

Retrieve comprehensive gene and transcript metadata from Ensembl, UniProt, and NCBI.

Parameters:

ens_ids: One or more Ensembl IDs (also supports WormBase, Flybase IDs). Limit: ~1000 IDs
-n/--ncbi: Disable NCBI data retrieval
-u/--uniprot: Disable UniProt data retrieval
-pdb: Include PDB identifiers (increases runtime)

Returns: UniProt ID, NCBI gene ID, primary gene name, synonyms, protein names, descriptions, biotype, canonical transcript

Examples:

# Get info for multiple genes
gget info ENSG00000034713 ENSG00000104853 ENSG00000170296

# Include PDB IDs
gget info ENSG00000034713 -pdb

# Python
gget.info(["ENSG00000034713", "ENSG00000104853"], pdb=True)

gget seq - Sequence Retrieval

Fetch nucleotide or amino acid sequences for genes and transcripts.

Parameters:

ens_ids: One or more Ensembl identifiers
-t/--translate: Fetch amino acid sequences instead of nucleotide
-iso/--isoforms: Return all transcript variants (gene IDs only)

Returns: FASTA format sequences

Examples:

# Get nucleotide sequences
gget seq ENSG00000034713 ENSG00000104853

# Get all protein isoforms
gget seq -t -iso ENSG00000034713

# Python
gget.seq(["ENSG00000034713"], translate=True, isoforms=True)

2. Sequence Analysis & Alignment

gget blast - BLAST Searches

BLAST nucleotide or amino acid sequences against standard databases.

Parameters:

sequence: Sequence string or path to FASTA/.txt file
-p/--program: blastn, blastp, blastx, tblastn, tblastx (auto-detected)
-db/--database:
- Nucleotide: nt, refseq_rna, pdbnt
- Protein: nr, swissprot, pdbaa, refseq_protein
-l/--limit: Max hits (default: 50)
-e/--expect: E-value cutoff (default: 10.0)
-lcf/--low_comp_filt: Enable low complexity filtering
-mbo/--megablast_off: Disable MegaBLAST (blastn only)

Examples:

# BLAST protein sequence
gget blast MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR

# BLAST from file with specific database
gget blast sequence.fasta -db swissprot -l 10

# Python
gget.blast("MKWMFK...", database="swissprot", limit=10)

gget blat - BLAT Searches

Locate genomic positions of sequences using UCSC BLAT.

Parameters:

sequence: Sequence string or path to FASTA/.txt file
-st/--seqtype: 'DNA', 'protein', 'translated%20RNA', 'translated%20DNA' (auto-detected)
-a/--assembly: Target assembly (default: 'human'/hg38; options: 'mouse'/mm39, 'zebrafinch'/taeGut2, etc.)

Returns: genome, query size, alignment positions, matches, mismatches, alignment percentage

Examples:

# Find genomic location in human
gget blat ATCGATCGATCGATCG

# Search in different assembly
gget blat -a mm39 ATCGATCGATCGATCG

# Python
gget.blat("ATCGATCGATCGATCG", assembly="mouse")

gget muscle - Multiple Sequence Alignment

Align multiple nucleotide or amino acid sequences using Muscle5.

Parameters:

fasta: Sequences or path to FASTA/.txt file
-s5/--super5: Use Super5 algorithm for faster processing (large datasets)

Returns: Aligned sequences in ClustalW format or aligned FASTA (.afa)

Examples:

# Align sequences from file
gget muscle sequences.fasta -o aligned.afa

# Use Super5 for large dataset
gget muscle large_dataset.fasta -s5

# Python
gget.muscle("sequences.fasta", save=True)

gget diamond - Local Sequence Alignment

Perform fast local protein or translated DNA alignment using DIAMOND.

Parameters:

Query: Sequences (string/list) or FASTA file path
--reference: Reference sequences (string/list) or FASTA file path (required)
--sensitivity: fast, mid-sensitive, sensitive, more-sensitive, very-sensitive (default), ultra-sensitive
--threads: CPU threads (default: 1)
--diamond_db: Save database for reuse
--translated: Enable nucleotide-to-amino acid alignment

Returns: Identity percentage, sequence lengths, match positions, gap openings, E-values, bit scores

Examples:

# Align against reference
gget diamond GGETISAWESQME -ref reference.fasta --threads 4

# Save database for reuse
gget diamond query.fasta -ref ref.fasta --diamond_db my_db.dmnd

# Python
gget.diamond("GGETISAWESQME", reference="reference.fasta", threads=4)

3. Structural & Protein Analysis

gget pdb - Protein Structures

Query RCSB Protein Data Bank for structure and metadata.

Parameters:

pdb_id: PDB identifier (e.g., '7S7U')
-r/--resource: Data type (pdb, entry, pubmed, assembly, entity types)
-i/--identifier: Assembly, entity, or chain ID

Returns: PDB format (structures) or JSON (metadata)

Examples:

# Download PDB structure
gget pdb 7S7U -o 7S7U.pdb

# Get metadata
gget pdb 7S7U -r entry

# Python
gget.pdb("7S7U", save=True)

gget alphafold - Protein Structure Prediction

Predict 3D protein structures using simplified AlphaFold2.

Setup Required:

# Install OpenMM first
uv pip install openmm

# Then setup AlphaFold
gget setup alphafold

Parameters:

sequence: Amino acid sequence (string), multiple sequences (list), or FASTA file. Multiple sequences trigger multimer modeling
-mr/--multimer_recycles: Recycling iterations (default: 3; recommend 20 for accuracy)
-mfm/--multimer_for_monomer: Apply multimer model to single proteins
-r/--relax: AMBER relaxation for top-ranked model
plot: Python-only; generate interactive 3D visualization (default: True)
show_sidechains: Python-only; include side chains (default: True)

Returns: PDB structure file, JSON alignment error data, optional 3D visualization

Examples:

# Predict single protein structure
gget alphafold MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR

# Predict multimer with higher accuracy
gget alphafold sequence1.fasta -mr 20 -r

# Python with visualization
gget.alphafold("MKWMFK...", plot=True, show_sidechains=True)

# Multimer prediction
gget.alphafold(["sequence1", "sequence2"], multimer_recycles=20)

gget elm - Eukaryotic Linear Motifs

Predict Eukaryotic Linear Motifs in protein sequences.

Setup Required:

gget setup elm

Parameters:

sequence: Amino acid sequence or UniProt Acc
-u/--uniprot: Indicates sequence is UniProt Acc
-e/--expand: Include protein names, organisms, references
-s/--sensitivity: DIAMOND alignment sensitivity (default: "very-sensitive")
-t/--threads: Number of threads (default: 1)

Returns: Two outputs:

ortholog_df: Linear motifs from orthologous proteins
regex_df: Motifs directly matched in input sequence

Examples:

# Predict motifs from sequence
gget elm LIAQSIGQASFV -o results

# Use UniProt accession with expanded info
gget elm --uniprot Q02410 -e

# Python
ortholog_df, regex_df = gget.elm("LIAQSIGQASFV")

4. Expression & Disease Data

gget archs4 - Gene Correlation & Tissue Expression

Query ARCHS4 database for correlated genes or tissue expression data.

Parameters:

gene: Gene symbol or Ensembl ID (with --ensembl flag)
-w/--which: 'correlation' (default, returns 100 most correlated genes) or 'tissue' (expression atlas)
-s/--species: 'human' (default) or 'mouse' (tissue data only)
-e/--ensembl: Input is Ensembl ID

Returns:

Correlation mode: Gene symbols, Pearson correlation coefficients
Tissue mode: Tissue identifiers, min/Q1/median/Q3/max expression values

Examples:

# Get correlated genes
gget archs4 ACE2

# Get tissue expression
gget archs4 -w tissue ACE2

# Python
gget.archs4("ACE2", which="tissue")

gget cellxgene - Single-Cell RNA-seq Data

Query CZ CELLxGENE Discover Census for single-cell data.

Setup Required:

gget setup cellxgene

Parameters:

--gene (-g): Gene names or Ensembl IDs (case-sensitive! 'PAX7' for human, 'Pax7' for mouse)
--tissue: Tissue type(s)
--cell_type: Specific cell type(s)
--species (-s): 'homo_sapiens' (default) or 'mus_musculus'
--census_version (-cv): Version ("stable", "latest", or dated)
--ensembl (-e): Use Ensembl IDs
--meta_only (-mo): Return metadata only
Additional filters: disease, development_stage, sex, assay, dataset_id, donor_id, ethnicity, suspension_type

Returns: AnnData object with count matrices and metadata (or metadata-only dataframes)

Examples:

# Get single-cell data for specific genes and cell types
gget cellxgene --gene ACE2 ABCA1 --tissue lung --cell_type "mucus secreting cell" -o lung_data.h5ad

# Metadata only
gget cellxgene --gene PAX7 --tissue muscle --meta_only -o metadata.csv

# Python
adata = gget.cellxgene(gene=["ACE2", "ABCA1"], tissue="lung", cell_type="mucus secreting cell")

gget enrichr - Enrichment Analysis

Perform ontology enrichment analysis on gene lists using Enrichr.

Parameters:

genes: Gene symbols or Ensembl IDs
-db/--database: Reference database (supports shortcuts: 'pathway', 'transcription', 'ontology', 'diseases_drugs', 'celltypes')
-s/--species: human (default), mouse, fly, yeast, worm, fish
-bkg_l/--background_list: Background genes for comparison
-ko/--kegg_out: Save KEGG pathway images with highlighted genes
plot: Python-only; generate graphical results

Database Shortcuts:

'pathway' → KEGG_2021_Human
'transcription' → ChEA_2016
'ontology' → GO_Biological_Process_2021
'diseases_drugs' → GWAS_Catalog_2019
'celltypes' → PanglaoDB_Augmented_2021

Examples:

# Enrichment analysis for ontology
gget enrichr -db ontology ACE2 AGT AGTR1

# Save KEGG pathways
gget enrichr -db pathway ACE2 AGT AGTR1 -ko ./kegg_images/

# Python with plot
gget.enrichr(["ACE2", "AGT", "AGTR1"], database="ontology", plot=True)

gget bgee - Orthology & Expression

Retrieve orthology and gene expression data from Bgee database.

Parameters:

ens_id: Ensembl gene ID or NCBI gene ID (for non-Ensembl species). Multiple IDs supported when type=expression
-t/--type: 'orthologs' (default) or 'expression'

Returns:

Orthologs mode: Matching genes across species with IDs, names, taxonomic info
Expression mode: Anatomical entities, confidence scores, expression status

Examples:

# Get orthologs
gget bgee ENSG00000169194

# Get expression data
gget bgee ENSG00000169194 -t expression

# Multiple genes
gget bgee ENSBTAG00000047356 ENSBTAG00000018317 -t expression

# Python
gget.bgee("ENSG00000169194", type="orthologs")

gget opentargets - Disease & Drug Associations

Retrieve disease and drug associations from OpenTargets.

Parameters:

Ensembl gene ID (required)
-r/--resource: diseases (default), drugs, tractability, pharmacogenetics, expression, depmap, interactions
-l/--limit: Cap results count
Filter arguments (vary by resource):
- drugs: --filter_disease
- pharmacogenetics: --filter_drug
- expression/depmap: --filter_tissue, --filter_anat_sys, --filter_organ
- interactions: --filter_protein_a, --filter_protein_b, --filter_gene_b

Examples:

# Get associated diseases
gget opentargets ENSG00000169194 -r diseases -l 5

# Get associated drugs
gget opentargets ENSG00000169194 -r drugs -l 10

# Get tissue expression
gget opentargets ENSG00000169194 -r expression --filter_tissue brain

# Python
gget.opentargets("ENSG00000169194", resource="diseases", limit=5)

gget cbio - cBioPortal Cancer Genomics

Plot cancer genomics heatmaps using cBioPortal data.

Two subcommands:

search - Find study IDs:

gget cbio search breast lung

plot - Generate heatmaps:

Parameters:

-s/--study_ids: Space-separated cBioPortal study IDs (required)
-g/--genes: Space-separated gene names or Ensembl IDs (required)
-st/--stratification: Column to organize data (tissue, cancer_type, cancer_type_detailed, study_id, sample)
-vt/--variation_type: Data type (mutation_occurrences, cna_nonbinary, sv_occurrences, cna_occurrences, Consequence)
-f/--filter: Filter by column value (e.g., 'study_id:msk_impact_2017')
-dd/--data_dir: Cache directory (default: ./gget_cbio_cache)
-fd/--figure_dir: Output directory (default: ./gget_cbio_figures)
-dpi: Resolution (default: 100)
-sh/--show: Display plot in window
-nc/--no_confirm: Skip download confirmations

Examples:

# Search for studies
gget cbio search esophag ovary

# Create heatmap
gget cbio plot -s msk_impact_2017 -g AKT1 ALK BRAF -st tissue -vt mutation_occurrences

# Python
gget.cbio_search(["esophag", "ovary"])
gget.cbio_plot(["msk_impact_2017"], ["AKT1", "ALK"], stratification="tissue")

gget cosmic - COSMIC Database

Search COSMIC (Catalogue Of Somatic Mutations In Cancer) database.

Important: License fees apply for commercial use. Requires COSMIC account credentials.

Parameters:

searchterm: Gene name, Ensembl ID, mutation notation, or sample ID
-ctp/--cosmic_tsv_path: Path to downloaded COSMIC TSV file (required for querying)
-l/--limit: Maximum results (default: 100)

Database download flags:

-d/--download_cosmic: Activate download mode
-gm/--gget_mutate: Create version for gget mutate
-cp/--cosmic_project: Database type (cancer, census, cell_line, resistance, genome_screen, targeted_screen)
-cv/--cosmic_version: COSMIC version
-gv/--grch_version: Human reference genome (37 or 38)
--email, --password: COSMIC credentials

Examples:

# First download database
gget cosmic -d --email [email protected] --password xxx -cp cancer

# Then query
gget cosmic EGFR -ctp cosmic_data.tsv -l 10

# Python
gget.cosmic("EGFR", cosmic_tsv_path="cosmic_data.tsv", limit=10)

5. Additional Tools

gget mutate - Generate Mutated Sequences

Generate mutated nucleotide sequences from mutation annotations.

Parameters:

sequences: FASTA file path or direct sequence input (string/list)
-m/--mutations: CSV/TSV file or DataFrame with mutation data (required)
-mc/--mut_column: Mutation column name (default: 'mutation')
-sic/--seq_id_column: Sequence ID column (default: 'seq_ID')
-mic/--mut_id_column: Mutation ID column
-k/--k: Length of flanking sequences (default: 30 nucleotides)

Returns: Mutated sequences in FASTA format

Examples:

# Single mutation
gget mutate ATCGCTAAGCT -m "c.4G>T"

# Multiple sequences with mutations from file
gget mutate sequences.fasta -m mutations.csv -o mutated.fasta

# Python
import pandas as pd
mutations_df = pd.DataFrame({"seq_ID": ["seq1"], "mutation": ["c.4G>T"]})
gget.mutate(["ATCGCTAAGCT"], mutations=mutations_df)

gget gpt - OpenAI Text Generation

Generate natural language text using OpenAI's API.

Setup Required:

gget setup gpt

Important: Free tier limited to 3 months after account creation. Set monthly billing limits.

Parameters:

prompt: Text input for generation (required)
api_key: OpenAI authentication (required)
Model configuration: temperature, top_p, max_tokens, frequency_penalty, presence_penalty
Default model: gpt-3.5-turbo (configurable)

Examples:

gget gpt "Explain CRISPR" --api_key your_key_here

# Python
gget.gpt("Explain CRISPR", api_key="your_key_here")

gget setup - Install Dependencies

Install/download third-party dependencies for specific modules.

Parameters:

module: Module name requiring dependency installation
-o/--out: Output folder path (elm module only)

Modules requiring setup:

alphafold - Downloads ~4GB of model parameters
cellxgene - Installs cellxgene-census (may not support latest Python)
elm - Downloads local ELM database
gpt - Configures OpenAI integration

Examples:

# Setup AlphaFold
gget setup alphafold

# Setup ELM with custom directory
gget setup elm -o /path/to/elm_data

# Python
gget.setup("alphafold")

Common Workflows

Workflow 1: Gene Discovery to Sequence Analysis

Find and analyze genes of interest:

# 1. Search for genes
results = gget.search(["GABA", "receptor"], species="homo_sapiens")

# 2. Get detailed information
gene_ids = results["ensembl_id"].tolist()
info = gget.info(gene_ids[:5])

# 3. Retrieve sequences
sequences = gget.seq(gene_ids[:5], translate=True)

Workflow 2: Sequence Alignment and Structure

Align sequences and predict structures:

# 1. Align multiple sequences
alignment = gget.muscle("sequences.fasta")

# 2. Find similar sequences
blast_results = gget.blast(my_sequence, database="swissprot", limit=10)

# 3. Predict structure
structure = gget.alphafold(my_sequence, plot=True)

# 4. Find linear motifs
ortholog_df, regex_df = gget.elm(my_sequence)

Workflow 3: Gene Expression and Enrichment

Analyze expression patterns and functional enrichment:

# 1. Get tissue expression
tissue_expr = gget.archs4("ACE2", which="tissue")

# 2. Find correlated genes
correlated = gget.archs4("ACE2", which="correlation")

# 3. Get single-cell data
adata = gget.cellxgene(gene=["ACE2"], tissue="lung", cell_type="epithelial cell")

# 4. Perform enrichment analysis
gene_list = correlated["gene_symbol"].tolist()[:50]
enrichment = gget.enrichr(gene_list, database="ontology", plot=True)

Workflow 4: Disease and Drug Analysis

Investigate disease associations and therapeutic targets:

# 1. Search for genes
genes = gget.search(["breast cancer"], species="homo_sapiens")

# 2. Get disease associations
diseases = gget.opentargets("ENSG00000169194", resource="diseases")

# 3. Get drug associations
drugs = gget.opentargets("ENSG00000169194", resource="drugs")

# 4. Query cancer genomics data
study_ids = gget.cbio_search(["breast"])
gget.cbio_plot(study_ids[:2], ["BRCA1", "BRCA2"], stratification="cancer_type")

# 5. Search COSMIC for mutations
cosmic_results = gget.cosmic("BRCA1", cosmic_tsv_path="cosmic.tsv")

Workflow 5: Comparative Genomics

Compare proteins across species:

# 1. Get orthologs
orthologs = gget.bgee("ENSG00000169194", type="orthologs")

# 2. Get sequences for comparison
human_seq = gget.seq("ENSG00000169194", translate=True)
mouse_seq = gget.seq("ENSMUSG00000026091", translate=True)

# 3. Align sequences
alignment = gget.muscle([human_seq, mouse_seq])

# 4. Compare structures
human_structure = gget.pdb("7S7U")
mouse_structure = gget.alphafold(mouse_seq)

Workflow 6: Building Reference Indices

Prepare reference data for downstream analysis (e.g., kallisto|bustools):

# 1. List available species
gget ref --list_species

# 2. Download reference files
gget ref -w gtf -w cdna -d homo_sapiens

# 3. Build kallisto index
kallisto index -i transcriptome.idx transcriptome.fasta

# 4. Download genome for alignment
gget ref -w dna -d homo_sapiens

Best Practices

Data Retrieval

Use --limit to control result sizes for large queries
Save results with -o/--out for reproducibility
Check database versions/releases for consistency across analyses
Use --quiet in production scripts to reduce output

Sequence Analysis

For BLAST/BLAT, start with default parameters, then adjust sensitivity
Use gget diamond with --threads for faster local alignment
Save DIAMOND databases with --diamond_db for repeated queries
For multiple sequence alignment, use -s5/--super5 for large datasets

Expression and Disease Data

Gene symbols are case-sensitive in cellxgene (e.g., 'PAX7' vs 'Pax7')
Run gget setup before first use of alphafold, cellxgene, elm, gpt
For enrichment analysis, use database shortcuts for convenience
Cache cBioPortal data with -dd to avoid repeated downloads

Structure Prediction

AlphaFold multimer predictions: use -mr 20 for higher accuracy
Use -r flag for AMBER relaxation of final structures
Visualize results in Python with plot=True
Check PDB database first before running AlphaFold predictions

Error Handling

Database structures change; update gget regularly: uv pip install --upgrade gget
Process max ~1000 Ensembl IDs at once with gget info
For large-scale analyses, implement rate limiting for API queries
Use virtual environments to avoid dependency conflicts

Output Formats

Command-line

Default: JSON
CSV: Add -csv flag
FASTA: gget seq, gget mutate
PDB: gget pdb, gget alphafold
PNG: gget cbio plot

Python

Default: DataFrame or dictionary
JSON: Add json=True parameter
Save to file: Add save=True or specify out="filename"
AnnData: gget cellxgene

Resources

This skill includes reference documentation for detailed module information:

references/

module_reference.md - Comprehensive parameter reference for all modules
database_info.md - Information about queried databases and their update frequencies
workflows.md - Extended workflow examples and use cases

For additional help:

Official documentation: https://pachterlab.github.io/gget/
GitHub issues: https://github.com/pachterlab/gget/issues
Citation: Luebbert, L. & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

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gget

Overview

Installation

Quick Start

Module Categories

1. Reference & Gene Information

gget ref - Reference Genome Downloads

gget search - Gene Search

gget info - Gene/Transcript Information

gget seq - Sequence Retrieval

2. Sequence Analysis & Alignment

gget blast - BLAST Searches

gget blat - BLAT Searches

gget muscle - Multiple Sequence Alignment

gget diamond - Local Sequence Alignment

3. Structural & Protein Analysis

gget pdb - Protein Structures

gget alphafold - Protein Structure Prediction

gget elm - Eukaryotic Linear Motifs

4. Expression & Disease Data

gget archs4 - Gene Correlation & Tissue Expression

gget cellxgene - Single-Cell RNA-seq Data

gget enrichr - Enrichment Analysis

gget bgee - Orthology & Expression

gget opentargets - Disease & Drug Associations

gget cbio - cBioPortal Cancer Genomics

gget cosmic - COSMIC Database

5. Additional Tools

gget mutate - Generate Mutated Sequences

gget gpt - OpenAI Text Generation

gget setup - Install Dependencies

Common Workflows

Workflow 1: Gene Discovery to Sequence Analysis

Workflow 2: Sequence Alignment and Structure

Workflow 3: Gene Expression and Enrichment

Workflow 4: Disease and Drug Analysis

Workflow 5: Comparative Genomics

Workflow 6: Building Reference Indices

Best Practices

Data Retrieval

Sequence Analysis

Expression and Disease Data

Structure Prediction

Error Handling

Output Formats

Command-line

Python

Resources

references/

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Source

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