He Dongze, Patro Rob
Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA.
bioRxiv. 2023 Mar 29:2023.03.28.534653. doi: 10.1101/2023.03.28.534653.
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 are being developed that can be accessed at https://combine-lab.github.io/alevin-fry-tutorials .
alevin-fry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，随着社区不断调整数据处理的最佳实践，以及随着alevin-fry生态系统自身的扩展和发展，在保持这些工具吸引力的性能和灵活性的同时，管理alevin-fry单细胞预处理工作流程的复杂性变得越来越重要。我们引入了simpleaf，这是一个使用alevin-fry生态系统中的工具简化单细胞数据处理的程序，并添加了新的功能和能力，同时保留了底层工具的灵活性和性能。
Simpleaf用Rust编写，并在BSD 3条款许可下发布。它可从其GitHub仓库https://github.com/COMBINE-lab/simpleaf免费获取，也可通过bioconda获取。Simpleaf的文档可在https://simpleaf.readthedocs.io/en/latest/获取，并且正在开发Simpleaf的教程，可在https://combine-lab.github.io/alevin-fry-tutorials访问。
