rsynthbio

rsynthbio is an R 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.

To generate datasets without code, use our web platform.

See the full documentation here.

For questions, suggestions, and support, email us at support@synthesize.bio.

How to Install

You can install rsynthbio from CRAN:

install.packages("rsynthbio")

To install the development version from GitHub:

remotes::install_github("synthesizebio/rsynthbio")

Authentication

Set up your API token (obtain one at app.synthesize.bio):

library(rsynthbio)

# Securely prompt for your token (recommended)
set_synthesize_token()

# Or store in system keyring for persistence across sessions
set_synthesize_token(use_keyring = TRUE)

# Load from keyring in future sessions
load_synthesize_token_from_keyring()

Quick Start

library(rsynthbio)

# See available models
list_models()

# Get an example query for bulk RNA-seq
query <- get_example_query(model_id = "gem-1-bulk")$example_query

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

# Access the results
metadata <- result$metadata
expression <- result$expression

Available Models

Model Type	Bulk	Single-Cell	Description
Baseline	gem-1-bulk	gem-1-sc	Generate expression from metadata
Reference Conditioning	gem-1-bulk_reference-conditioning	gem-1-sc_reference-conditioning	Generate expression anchored to a reference sample
Metadata Prediction	gem-1-bulk_predict-metadata	gem-1-sc_predict-metadata	Predict metadata from expression

Only baseline models are available to all users. You can check which models are available programmatically, use list_models(). Contact us at support@synthesize.bio if you have any questions.

Documentation

For detailed usage instructions, see the vignettes:

• Getting Started — Installation, authentication, and overview
• Baseline Models — Generate expression from metadata
• Reference Conditioning — Condition on real expression data
• Metadata Prediction — Infer metadata from expression

Mintlify source

This repo now also includes public Mintlify-compatible docs source under docs-external/ so the shared docs site can aggregate the R SDK docs directly from rsynthbio.

• vignettes/*.Rmd and _pkgdown.yml remain the primary authored docs inputs
• man/*.Rd remains the source for generated function-level reference docs
• scripts/generate_mintlify_docs.py regenerates the committed Mintlify output tree

Regenerate the Mintlify docs after changing vignettes, package exports, or roxygen docs:

python3 scripts/generate_mintlify_docs.py

The generated pages are committed in docs-external/ so changes are reviewable in PRs. pkgdown stays in place during the transition, and GitHub Pages remains the current public docs host until the shared docs site is ready to switch over.

Rate Limits

Free usage of Synthesize Bio is limited. If you exceed this limit, you will receive an error message. To generate more samples, please contact us at support@synthesize.bio.