DoTools: a cross platform framework to streamline common single cell workflows

<h4>Motivation</h4>Throughout the years, single-cell RNA sequencing (scRNA-seq) has become a standard approach for characterising transcriptomic changes associated with diseases and other biological conditions. However, the rapid expansion of tools and algorithms developed in various programming languages has made single-cell data analysis increasingly complex. In particular, integrating multiple tools into a single workflow often demands substantial learning time and coding expertise.<h4>Results</h4>To address these challenges, we developed DoTools, a unified framework for R/Bioconductor and Python/PyPI that simplifies the integration of third-party tools such as scVI, CellTypist, and CellBender into standard pipelines like Seurat, SingleCellExperiment and Scanpy. DoTools provides advanced cross-language wrappers and visualisation utilities to streamline data preprocessing, quality control, cell type annotation, and downstream analysis, while implementing best practices in scRNA-seq analysis regardless of the computational language. Its modular design and compatibility with widely used bioinformatics environments makes it accessible and valuable to both novice and experienced data scientists.<h4>Availability and implementation</h4>DoTools is freely available for R and Python at Bioconductor and PyPI (https://bioconductor.org/packages/release/bioc/html/DOtools.html and https://pypi.org/project/DoTools-py/), the developmental versions of DoTools are maintained on GitHub (https://github.com/MarianoRuzJurado/DoTools and https://github.com/davidrm-bio/DoTools_py).