The article introduces deepTools2, an updated version of a Galaxy-based web server for processing and visualizing deep-sequencing data. DeepTools2 offers a comprehensive set of tools for quality control, data processing, normalization, integration, and visualization. Key enhancements include new quality control tools like plotCoverage and plotPCA, improved data processing flexibility and speed, and enhanced integrative analyses with tools like computeMatrix and plotHeatmap. The web server is freely available at deeptools.ie-freiburg.mpg.de and can be easily deployed within any Galaxy framework. DeepTools2 also provides a public API and command-line usage options, making it accessible to a wide range of users. The authors highlight the benefits of the Galaxy platform for reproducible and standardized analysis workflows, emphasizing the software's suitability for large-scale data production and single-cell sequencing.The article introduces deepTools2, an updated version of a Galaxy-based web server for processing and visualizing deep-sequencing data. DeepTools2 offers a comprehensive set of tools for quality control, data processing, normalization, integration, and visualization. Key enhancements include new quality control tools like plotCoverage and plotPCA, improved data processing flexibility and speed, and enhanced integrative analyses with tools like computeMatrix and plotHeatmap. The web server is freely available at deeptools.ie-freiburg.mpg.de and can be easily deployed within any Galaxy framework. DeepTools2 also provides a public API and command-line usage options, making it accessible to a wide range of users. The authors highlight the benefits of the Galaxy platform for reproducible and standardized analysis workflows, emphasizing the software's suitability for large-scale data production and single-cell sequencing.