R Observatory: Metrics for rsynthbio version 4.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rsynthbio

4.2.3Package record

Synthesize Bio API Wrapper

0packages depend

3.9Kdownloads / year

76.2%test coverage

13/13flavors OK

Overview

About

Maintained by Alex DavidCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 4.2.3

Format hosted GEM-2 baseline, reference-based expression, metadata prediction and reconstruction results through the standard prediction client.
Preserve nested metadata, classifier labels/probabilities and full numeric precision when reading prediction results.
Keep requested input/output column order and missing values aligned.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("rsynthbio", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("synthesizebio/rsynthbio")

Development version from synthesizebio/rsynthbio. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rsynthbio

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rsynthbio

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-rsynthbio

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 4.2.3

READMEYes · 730 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 4.2.3Citation fileNo

Help pages: 12
Examples that run: 0%7 never run
Exported functions with examples: 58%
Documented parameters: 100%
Return-value docs: 58%
Help pages citing references: 0%

Vignettes (6)

How these are measured

Downloads

3.9K

CRAN downloads in the past year

Rank #11,456 · ~11/day · ~323/mo

Releases R versions

Daily download trend is not available in this view yet.

43930 days

95090 days

3.9K1 year

Compare downloads with other packages →

Also on121 r2u2 autocran

How downloads are counted

Repository

synthesizebio/rsynthbio ↗Organization: synthesizebio

3Stars

1Forks

0Open issues

1Open PRs

6Releases

49Commits

8Commit identities

49 commits · Last activity 2026-10-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 84%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2026-07-14 · 22026-07-22 · 3

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/synthesizebio/rsynthbio on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (2)

Issue templatesPR template

Docs source (2)

GitHub Pages site last deployed 2026-05-06 · The repository has a site deploy workflow

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Cursorfirst seen 2026-03-31
Seen in the repository: .cursor
Named in .Rbuildignore: .cursor
Commits: at least 3 crediting it in the message

Review tools

Gemini Code Assist
Seen in the repository: .gemini

From outside contributors

Cursor
Pull requests: 9 from outside contributors, first on 2026-04-14

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing rsynthbio adds 13 packages (10 with compiled code, 3.7 MB of source tarballs). Heaviest: openssl 1.1 MB, jsonlite 1.0 MB, curl 714 KB.

Depends (0)

none

Imports (4)

getPass keyring jsonlite httr

LinkingTo (0)

none

Suggests (5)

rmarkdown knitr testthat mockery arrow

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (2)

Alex David

Author, Maintainer since 4.2.2 (2026) · added in 4.2.2

Synthesize Bio

Author · added in 4.0.0

Previously maintained by Synthesize Bio (4.0.0 to 4.2.1) and Candace Savonen (1.0.0 to 3.0.2).

Listed in earlier versions (1)

Candace Savonen

no longer listed · 1.0.0 to 3.0.2

Releases (12)

Pick two releases to compare their code metrics.

4.2.3Latest
record
2026-10-17 · current release · diff ↗ ·
20 hours in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-17 02:21 to 2026-10-17 21:55 UTC, in 7 readings.
4.2.2
record
2026-10-14 · diff ↗
4.2.1
record
2026-10-13 · diff ↗
4.2.0
record
2026-06-12 · diff ↗ ·
added 1 export
SELF_HOSTED_TIMEOUT
R
R 4.6.0 released · 2026-04-24
4.1.0
record
2026-02-25 · diff ↗
4.0.1
record
2026-02-13 · diff ↗
4.0.0
record
2025-12-04 · diff ↗ ·
removed 8 exports
MODEL_MODALITIES, MODEL_MODES, get_valid_modalities, get_valid_modes, get_valid_query, log_cpm, validate_modality, validate_query

added 2 exports
get_example_query, list_models
3.0.2
record
2025-10-29 · diff ↗ ·
removed 1 export
extract_expression_data

added 1 export
MODEL_MODES
3.0.0
record
2025-10-15 · diff ↗ ·
added 3 exports
DEFAULT_POLL_INTERVAL_SECONDS, DEFAULT_POLL_TIMEOUT_SECONDS, DEFAULT_TIMEOUT
2.2.1
record
2025-09-12 · diff ↗
2.0.0
record
2025-06-04 · diff ↗ ·
added 1 export
get_valid_modes
1.0.0
record
2025-06-02
R
R 4.5.0 released · 2025-04-11

Across CRAN, the median accepted release of the past year spent 22 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2025-06-02
Total releases: 12 / 1 yrs
License: MIT + file LICENSE OSI
Download size: 86 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rsynthbio")

Format

David, A., & Synthesize Bio. (2026). rsynthbio: Synthesize Bio API Wrapper (Version 4.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.rsynthbio

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rsynthbio version 4.2.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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