pysynthbio 4.1.0

A package to retrieve data and models from Synthesize Bio's API

 pysynthbio

pysynthbio is an Python package that provides a convenient interface to the Synthesize Bio API, allowing users to generate realistic gene expression data based on specified biological conditions. This package enables researchers to easily access AI-generated transcriptomic data for various modalities including bulk RNA-seq and single-cell RNA-seq.

If you'd prefer 1-click dataset generation and analysis, try our web platform.

Prerequisites

Create a Synthesize Bio account and generate an API Key.

Installation

pip install pysynthbio

Quickstart

import pysynthbio

# Set your API token (or use environment variable SYNTHESIZE_API_KEY)
pysynthbio.set_synthesize_token(use_keyring=True)

# Get an example query for the bulk RNA-seq baseline model
query = pysynthbio.get_example_query(model_id="gem-1-bulk")["example_query"]

# Generate synthetic expression data
result = pysynthbio.predict_query(query, model_id="gem-1-bulk")

# Access the results
metadata = result["metadata"]
expression = result["expression"]

Documentation

Get Started | Full Documentation

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