Overview | Available Models | Creating a Query | Making a Prediction | Single-Cell Example | Query Parameters | sampling_strategy (character, required) | total_count (integer, optional) | deterministic_latents (logical, optional) | seed (integer, optional) | Combining Parameters | Valid Metadata Keys | Biological | Perturbational | Technical | Valid Metadata Values | Modifying Query Inputs | Working with Results
Package: rsynthbio 4.2.3
Alex David
rsynthbio: Synthesize Bio API Wrapper
Access Synthesize Bio models from their API <https://app.synthesize.bio/> using this wrapper 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.
Authors:
rsynthbio_4.2.3.tar.gz
rsynthbio_4.2.3.zip(r-4.7-any)rsynthbio_4.2.3.zip(r-4.6-any)rsynthbio_4.2.3.zip(r-4.5-any)
rsynthbio_4.2.3.tgz(r-4.6-any)rsynthbio_4.2.3.tgz(r-4.5-any)
rsynthbio_4.2.3.tar.gz(r-4.7-any)rsynthbio_4.2.3.tar.gz(r-4.6-any)
rsynthbio_4.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rsynthbio/json (API)
| # Install 'rsynthbio' in R: |
| install.packages('rsynthbio', repos = c('https://synthesizebio.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/synthesizebio/rsynthbio/issues
Last updated from:9343cda9cd. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 175 | ||
| source / vignettes | OK | 236 | ||
| linux-release | OK | 173 | ||
| macos-release | OK | 93 | ||
| macos-oldrel | OK | 103 | ||
| windows-devel | OK | 78 | ||
| windows-release | OK | 84 | ||
| windows-oldrel | OK | 80 | ||
| wasm-release | OK | 128 |
Exports:API_BASE_URLclear_synthesize_tokenDEFAULT_POLL_INTERVAL_SECONDSDEFAULT_POLL_TIMEOUT_SECONDSDEFAULT_TIMEOUTget_example_queryhas_synthesize_tokenlist_modelsload_synthesize_token_from_keyringpredict_querySELF_HOSTED_TIMEOUTset_synthesize_token
Dependencies:askpasscurlfilelockgetPasshttrjsonlitekeyringmimeopensslR6rstudioapisysyaml
Baseline Models
Last update: 2026-10-13
Started: 2025-12-19
Getting Started
How to install | Authentication | Available Model Types | Baseline Models | Reference Conditioning Models | Metadata Prediction Models | Listing Available Models | Exploring Available Metadata | Quick Start | Session info | Additional Resources
Last update: 2026-10-13
Started: 2025-05-13
Self-Hosted Models
How it differs from the hosted path | Installation | Enabling self-hosted mode | Pointing each model at its container | Resolution precedence | Authentication (optional) | Raw responses | Session info
Last update: 2026-06-11
Started: 2026-06-11
Available Metadata
Overview
Last update: 2026-04-22
Started: 2026-04-22
Reference Conditioning
Overview | Available Models | How It Works | Creating a Query | Perturbation-Only Metadata | Example: Simulating a Drug Treatment | Example: CRISPR Knockout Simulation | Query Parameters | conditioning (list, optional) | sampling_strategy (character, required) | fixed_total_count (logical, optional) | total_count (integer, optional) | deterministic_latents (logical, optional) | seed (integer, optional) | Valid Perturbation Metadata | Working with Results | Differential Expression | Important Notes | Counts Vector Length | Gene Order
Last update: 2026-02-23
Started: 2025-12-19
Metadata Prediction
Overview | Available Models | How It Works | Creating a Query | Example: Predicting Sample Metadata | Example: Single Sample Prediction | Query Parameters | inputs (list, required) | seed (integer, optional) | Understanding the Results | Predicted Metadata | Classifier Probabilities | Latent Representations | Use Cases | Sample Annotation | Quality Control | Important Notes | Counts Vector Length | Gene Order | Non-Negative Counts
Last update: 2026-01-07
Started: 2025-12-19
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| API Base URL | API_BASE_URL |
| Clear Synthesize Bio API Token | clear_synthesize_token |
| Default Poll Interval | DEFAULT_POLL_INTERVAL_SECONDS |
| Default Poll Timeout | DEFAULT_POLL_TIMEOUT_SECONDS |
| Default Timeout | DEFAULT_TIMEOUT |
| Get Example Query for Model | get_example_query |
| Check if Synthesize Bio API Token is Set | has_synthesize_token |
| List Available Models | list_models |
| Load Synthesize Bio API Token from Keyring | load_synthesize_token_from_keyring |
| Predict Gene Expression | predict_query |
| Self-Hosted Timeout | SELF_HOSTED_TIMEOUT |
| Set Synthesize Bio API Token | set_synthesize_token |