SC-Framework: A robust and FAIR semi-interactive environment for single-cell resolution datasets
Schultheis, H.; Detleffsen, J.; Wiegandt, R.; Bentsen, M.; Alayoubi, Y.; Valente, G.; Kessler, M. F.; Bruns, B.; Mirza, D.; Usanayo, A.; Walter, J.; Goymann, P.; Hobein, M.; Kuenne, C.; Looso, M.
Show abstract
The accelerated development of single-cell technologies has profoundly impacted the field of biological research, facilitating unparalleled insights into cellular heterogeneity. However, this progress has also produced new computational challenges in the field of bioinformatics: single-cell datasets are increasingly high-dimensional, multimodal, and large-scale, while analysis workflows often remain fragmented, data type specific, ad hoc, and difficult to reproduce. The prevailing methodologies are dependent on a combination of public tools, which hinders the reproducibility of results, limits scalability, and complicates the efforts to establish benchmarks. The necessity for a higher-level, unified framework for single-cell data analysis is paramount to address these inherent limitations. Here, we introduce the SC-Framework, providing the integration of standardized data structures, declarative workflows and standardized computational backends in a containerized environment, enabling analysts to focus on biological interpretation rather than technical overhead. SC-Framework is available at GitHub (https://github.com/loosolab/SC-Framework).
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