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Releases: Novartis/tinydenseR

tinydenseR 0.0.1.0013 — Legacy API (preprint‑compatible)

12 Jan 15:02
@PedroMilanezAlmeida PedroMilanezAlmeida
0.0.1.0013
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Summary
This first public release captures the legacy API of tinydenseR used in the preprint so that results remain reproducible and citable. The package provides a landmark‑based, sample‑centric workflow for single‑cell analysis with built‑in visualization and support for scRNA‑seq and cytometry data.

Why this release

  • Ensures a stable tag that matches the preprint for benchmarking and reproduction.
  • Provides a clear baseline before introducing the upcoming, redesigned API.
  • Establishes semantic versioning for future development.

Highlights

  • Sample‑centric modeling: treats samples (not cells) as biological replicates for robust statistics.
  • Scalable & memory‑efficient: suitable for atlas‑scale datasets.
  • Technology‑agnostic: works with scRNA‑seq, flow, and mass cytometry.
  • Built‑in plots & vignettes to explore landmark geometry, differential abundance/expression.

API status

  • This tag preserves the legacy API used by the preprint.
  • Breaking changes are planned for the next release (new API).
  • No deprecations were introduced in 0.0.1.0013; the legacy functions remain as‑is.

Compatibility

  • Requires R ≥ 4.1.
  • Tested on Linux and macOS with typical single‑cell pipelines.

Installation

# Install the legacy API exactly as used in the preprint:
if (!require("devtools")) install.packages("devtools")
devtools::install_github("Novartis/tinydenseR@0.0.1.0013")

Documentation & examples
See the repository README and vignettes for quick‑start examples, background, and detailed workflow description. Novartis/tinydenseR GitHub

Known limitations

  • Expect breaking changes in naming/arguments in the next release to streamline the workflow.

Citation
If you use tinydenseR, please cite the preprint:
“Sample‑level modeling of single‑cell data at scale with tinydenseR” — bioRxiv, DOI 10.1101/2025.11.26.690752. View on bioRxiv

Acknowledgments
Thanks to the contributors and reviewers within Novartis Biomedical Research and the single‑cell community for feedback leading up to this release.

Full Changelog: https://github.com/Novartis/tinydenseR/commits/0.0.1.0013

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