---
title: "Getting Started"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE # Set to FALSE since API calls require credentials
)
```


`rsynthbio` is an R 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.

Alternatively, you can AI generate datasets from our [web platform](https://app.synthesize.bio/datasets/).

## How to install

You can install `rsynthbio` from CRAN:

```{r installation, eval=FALSE}
install.packages("rsynthbio")
```

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

```{r github-installation, eval=FALSE}
if (!("remotes" %in% installed.packages())) {
  install.packages("remotes")
}
remotes::install_github("synthesizebio/rsynthbio")
```

Once installed, load the package:

```{r}
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:

```{r auth-secure, eval=FALSE}
# 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.

```{r, eval=FALSE}
# In future sessions, load the stored token
load_synthesize_token_from_keyring()

# Check if a token is already set
has_synthesize_token()
```

You can manually set the token, but don't commit it to version control!
```{r, eval=FALSE}
set_synthesize_token(token = "your-token-here")
```

You can obtain an API token by registering at [Synthesize Bio](https://app.synthesize.bio).

## Available Model Types

Synthesize Bio provides several types of models for different use cases:

### Baseline Models

Generate synthetic gene expression data from metadata alone. You describe the biological conditions (tissue type, disease state, perturbations, etc.) and the model generates realistic expression profiles.

- **`gem-1-bulk`**: Bulk RNA-seq baseline model
- **`gem-1-sc`**: Single-cell RNA-seq baseline model

See the [Baseline Models](baseline.html) vignette for detailed usage.

### Reference Conditioning Models

Generate expression data conditioned on a real reference sample. This allows you to "anchor" to an existing expression profile while applying perturbations or modifications.

- **`gem-1-bulk_reference-conditioning`**: Bulk RNA-seq reference conditioning model
- **`gem-1-sc_reference-conditioning`**: Single-cell RNA-seq reference conditioning model

See the [Reference Conditioning](reference-conditioning.html) vignette for detailed usage.

### Metadata Prediction Models

Infer metadata from observed expression data. Given a gene expression profile, predict the likely biological characteristics (cell type, tissue, disease state, etc.).

- **`gem-1-bulk_predict-metadata`**: Bulk RNA-seq metadata prediction model
- **`gem-1-sc_predict-metadata`**: Single-cell RNA-seq metadata prediction model

See the [Metadata Prediction](metadata-prediction.html) vignette for detailed usage.

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.

### Listing Available Models

You can check which models are available programmatically:

```{r models}
# Check available models
list_models()
```

### Exploring Available Metadata

Each model accepts a specific set of metadata fields with defined vocabularies (valid ontology IDs, cell lines, tissues, etc.). You can browse and download these vocabularies at [app.synthesize.bio/docs/vocab](https://app.synthesize.bio/docs/vocab).

See the [Available Metadata](available-metadata.html) vignette for more details.

## Quick Start

Here's a quick example using a baseline model:
```{r query, eval=FALSE}
# Get an example query structure
query <- get_example_query(model_id = "gem-1-bulk")$example_query

# Submit the query and get results
result <- predict_query(query, model_id = "gem-1-bulk")

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

For more detailed examples and advanced usage, see the model-specific vignettes linked above.

## Session info

```{r session-info}
sessionInfo()
```

## Additional Resources

- [Package Source Code](https://github.com/synthesizebio/rsynthbio)
- [File Bug Reports](https://github.com/synthesizebio/rsynthbio/issues)
