Metadata-Version: 2.4
Name: pysynthbio
Version: 4.2.2
Summary: A package to retrieve data and models from Synthesize Bio's API
Author: Alex David, Candace Savonen
License-Expression: MIT
Project-URL: Homepage, https://github.com/synthesizebio/pysynthbio
Project-URL: Issues, https://github.com/synthesizebio/pysynthbio/issues
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=2.2.5
Requires-Dist: pandas>=2.2.3
Requires-Dist: requests
Requires-Dist: keyring>=23.0.0
Provides-Extra: secure
Requires-Dist: keyring>=23.0.0; extra == "secure"
Provides-Extra: self-hosted
Requires-Dist: pyarrow>=15.0.0; extra == "self-hosted"
Provides-Extra: all
Requires-Dist: keyring>=23.0.0; extra == "all"
Requires-Dist: pyarrow>=15.0.0; extra == "all"
Provides-Extra: dev
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: black>=26.3.1; extra == "dev"
Requires-Dist: build; extra == "dev"
Dynamic: license-file

# <img src="https://assets.synthesize.bio/logomark.png" style="width: 30px; height: 30px;" alt="Logomark">&nbsp;pysynthbio

`pysynthbio` is an Python package that provides a convenient interface to the [Synthesize Bio](https://www.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](https://app.synthesize.bio/datasets/).

## Prerequisites

Create a [Synthesize Bio](https://app.synthesize.bio/) account and generate an [API Key](https://app.synthesize.bio/account/api-keys).

## Installation

```
pip install pysynthbio
```

## Quickstart

```python
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

The canonical pysynthbio docs live at [docs.synthesize.bio/pysynthbio](https://docs.synthesize.bio/pysynthbio).

- [Get started](https://docs.synthesize.bio/pysynthbio/getting-started)
- [Installation](https://docs.synthesize.bio/pysynthbio/installation)
- [Models](https://docs.synthesize.bio/pysynthbio/models/baseline)

The legacy GitHub Pages site at `synthesizebio.github.io/pysynthbio` redirects to the new URLs and is no longer updated. The MDX source for the customer-facing docs lives in [`docs-external/`](./docs-external) and is aggregated into [`docs-external`](https://github.com/synthesizebio/docs-external) by the Mintlify multirepo workflow.

## Questions? Suggestions? Support?

Email us at [support@synthesize.bio](mailto:support@synthesize.bio). We'd love to hear from you!
