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gs2txt Documentation

Installation

Installation¶

Requirements¶

Python 3.9 or higher
pip package manager

Basic Installation¶

Install gs2txt from PyPI:

pip install gs2txt

Installation with Optional Dependencies¶

With Enrichment Support¶

For built-in pathway enrichment using GSEApy:

pip install gs2txt[enrichment]

With All Features¶

pip install gs2txt[all]

For Development¶

pip install gs2txt[dev]

Development Installation¶

Clone the repository and install in editable mode:

git clone https://github.com/wuys13/gs2txt.git
cd gs2txt
pip install -e ".[dev]"

Verify Installation¶

import gs2txt
from gs2txt import GeneSetAnnotator
from gs2txt.llm import OpenAIProvider, AnthropicProvider, LiteLLMProvider

print("gs2txt installed successfully!")

API Keys¶

gs2txt requires an API key for the LLM provider you choose:

OpenAI¶

export OPENAI_API_KEY=sk-xxx

Anthropic¶

export ANTHROPIC_API_KEY=sk-ant-xxx

LiteLLM (Recommended)¶

export LITELLM_API_KEY=your-api-key

Next Steps¶