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, single-cell RNA-seq, microarray data, and more.

See the full documentation pages here.

How to install

You can install rsynthbio from CRAN:

install.packages("rsynthbio")

If you want the development version, you can install using the remotes package to install from GitHub:

if (!("remotes" %in% installed.packages())) {
  install.packages("remotes")
}
remotes::install_github("synthesizebio/rsynthbio")

Once installed, load the package:

library(rsynthbio)

Authentication

Before using the Synthesize Bio API, you need to set up your API token. The package provides a secure way to handle authentication:

# Securely prompt for and store your API token
# The token will not be visible in the console
set_synthesize_token()

# You can also store the token in your system keyring for persistence
# across R sessions (requires the 'keyring' package)
set_synthesize_token(use_keyring = TRUE)

Loading your API key for a session.

# In future sessions, load the stored token
load_synthesize_token_from_keyring()

# Check if a token is already set
has_synthesize_token()

You can obtain an API token by registering at Synthesize Bio.

Security Best Practices

For security reasons, remember to clear your token when you’re done:

# Clear token from current session
clear_synthesize_token()

# Clear token from both session and keyring
clear_synthesize_token(remove_from_keyring = TRUE)

Never hard-code your token in scripts that will be shared or committed to version control.

Basic Usage

Available Modalities

The package supports various data modalities. You can view all available modalities with:

# Check available modalities
get_valid_modalities()

Creating a Query

The first step to generating AI-generated gene expression data is to create a query. The package provides a sample query that you can modify:

# Get a sample query
query <- get_valid_query()

# Inspect the query structure
str(query)

The query consists of:

1. output_modality: The type of gene expression data to generate
2. mode: The prediction mode (e.g., “mean estimation”)
3. inputs: A list of biological conditions to generate data for

# Request raw counts data
result <- predict_query(query)

# Structure of the result
result

Releases

These docs are specific to Version 2.x.x of the pysynthbio API. Note that the versioning for this package runs parallel to the versioning of the AI models from Synthesize Bio.

The major releases indicate what model from the API is being used. So 2.x.x means v2.0 from the API is being used. Whereas the .x.x part is related to the package releases/bug fixes, etc.