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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 if you have any questions.

Documentation

For detailed usage instructions, see the vignettes:

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.