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rsynthbio

An API wrapper package

https://github.com/synthesizebio/rsynthbio

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (16.3%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

An API wrapper package

Basic Info
Statistics
  • Stars: 0
  • Watchers: 8
  • Forks: 0
  • Open Issues: 1
  • Releases: 3
Created about 1 year ago · Last pushed 10 months ago
Metadata Files
Readme Changelog License

README.md

rsynthbio Logomark

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.

Alternatively, you can AI generate datasets from our platform website.

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

setsynthesizetoken()

You can also store the token in your system keyring for persistence

across R sessions (requires the 'keyring' package)

setsynthesizetoken(use_keyring = TRUE) ```

Loading your API key for a session.

```

In future sessions, load the stored token

loadsynthesizetokenfromkeyring()

Check if a token is already set

hassynthesizetoken() ```

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

clearsynthesizetoken()

Clear token from both session and keyring

clearsynthesizetoken(removefromkeyring = 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

getvalidmodalities() ```

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 <- getvalidquery()

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 ```

Rate limits

Free usage of Synthesize Bio is limited. If you exceed this limit you may recieve an error message stating you've exceeded your limit. To generate more samples, please contact us at info@synthesize.bio for more information.

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.

Owner

  • Name: Synthesize Bio
  • Login: synthesizebio
  • Kind: organization
  • Location: United States of America

GitHub Events

Total
  • Release event: 2
  • Delete event: 6
  • Issue comment event: 3
  • Push event: 34
  • Public event: 1
  • Pull request review comment event: 3
  • Pull request review event: 19
  • Pull request event: 16
  • Create event: 11
Last Year
  • Release event: 2
  • Delete event: 6
  • Issue comment event: 3
  • Push event: 34
  • Public event: 1
  • Pull request review comment event: 3
  • Pull request review event: 19
  • Pull request event: 16
  • Create event: 11

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 0
  • Total pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Total issue authors: 0
  • Total pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.3
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 10
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 0.3
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • cansavvy (8)
  • awalsh17 (1)
  • alexanderadavid (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 368 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: rsynthbio

Synthesize Bio API Wrapper

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 368 Last month
Rankings
Dependent packages count: 26.4%
Dependent repos count: 32.5%
Average: 48.5%
Downloads: 86.6%
Maintainers (1)
cansav09@gmail.com
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/publish_to_cran.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
  • softprops/action-gh-release v1 composite
DESCRIPTION cran
  • dplyr * imports
  • getPass * imports
  • httr * imports
  • jsonlite * imports
  • keyring * imports
  • purrr * imports
  • tibble * imports
  • tidyr * imports
  • knitr * suggests
  • mockery * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests