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arXiv · 2508.08014

ShortCake: An integrated platform for efficient and reproducible single-cell analysis

Ryuichiro Nakato·Luis Augusto Eijy Nagai
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Abstract

Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For the research community, minimizing the time spent on environment setup and installation issues is essential. Results: We present ShortCake, a containerized platform that integrates a suite of single-cell analysis tools written in R and Python. ShortCake isolates competing Python tools into separate virtual environments that can be easily accessed within a Jupyter notebook. This enables users to effortlessly transition between various environments, including R, even within a single notebook. Additionally, ShortCake offers multiple ``flavors,'' enabling users to select container images tailored to their specific needs. ShortCake provides a unified environment with fixed versions of various tools, thus streamlining workflows, reducing setup time, and improving reproducibility. Availability and implementation: The ShortCake image is available on DockerHub (https://hub.docker.com/r/rnakato/shortcake). The source code is available on GitHub (https://github.com/rnakato/ShortCake).

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Ryuichiro Nakato, Luis Augusto Eijy Nagai. 2025-08-11. ShortCake: An integrated platform for efficient and reproducible single-cell analysis. https://arxiv.org/abs/2508.08014

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