Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, United States.
Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, United States.
Bioinformatics. 2023 Oct 3;39(10). doi: 10.1093/bioinformatics/btad614.
The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell data processing. However, as new single-cell technologies are introduced, as the community continues to adjust best practices for data processing, and as the alevin-fry ecosystem itself expands and grows, it is becoming increasingly important to manage the complexity of alevin-fry's single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.
Simpleaf is written in Rust and released under a BSD 3-Clause license. It is freely available from its GitHub repository https://github.com/COMBINE-lab/simpleaf, and via bioconda. Documentation for simpleaf is available at https://simpleaf.readthedocs.io/en/latest/ and tutorials for simpleaf that have been developed can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.
幼鱼 - 鱼苗生态系统为单细胞数据处理提供了一套强大且不断发展的程序。然而，随着新的单细胞技术的引入，随着社区继续调整数据处理的最佳实践，以及幼鱼 - 鱼苗生态系统自身的扩展和增长，管理幼鱼 - 鱼苗单细胞预处理工作流程的复杂性变得越来越重要，同时保持这些工具的吸引力的性能和灵活性。我们引入了 simpleaf，这是一个使用幼鱼 - 鱼苗生态系统中的工具简化单细胞数据处理的程序，并增加了新的功能和功能，同时保留了底层工具的灵活性和性能。
simpleaf 是用 Rust 编写的，并根据 BSD 3-Clause 许可证发布。它可以从其 GitHub 存储库 https://github.com/COMBINE-lab/simpleaf 以及 bioconda 免费获得。simpleaf 的文档可在 https://simpleaf.readthedocs.io/en/latest/ 获得，并且可以访问在 https://combine-lab.github.io/alevin-fry-tutorials 开发的 simpleaf 教程。
