simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.
simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry.
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simpleaf：使用 alevin-fry 进行单细胞转录组数据处理的简单、灵活且可扩展的框架。
DOI：
10.1101/2023.03.28.534653
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Patro,Rob
中科院分区：
文献类型：
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作者：
He,Dongze;Patro,Rob
摘要Thallevin-fryEcology为单细胞数据处理提供了一套强大且不断增长的程序。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Aevin-Fry生态系统本身的扩展和发展，管理Aevin-Fry单细胞前处理工作流程的复杂性变得越来越重要，同时保持使这些工具具有吸引力的性能和灵活性。我们介绍了Simpleaf，这是一个程序，它使用来自生态系统的工具简化了单细胞数据的处理，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。可用性和实现Simpleaf是用Rust编写的，并在BSD 3条款许可证下发布。它可以从GitHub存储库https://github.com/COMBINE-lab/simpleaf，或通过BioConda免费获得。Https://simpleaf.readthedocs.io/en/latest/上提供了Simple的文档，已经开发的Simple的教程可以在https://combine-lab.github.io/alevin-fry-tutorials.上访问
SummaryThealevin-fryecosystem 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 thealevin-fryecosystem itself expands and grows, it is becoming increasingly important to manage the complexity ofalevin-fry’s single-cell preprocessing workflows while retaining the performance and flexibility that make these tools enticing. We introducesimpleaf, a program that simplifies the processing of single-cell data using tools from thealevin-fryecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.Availability and implementationSimpleafis 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 forsimpleafis available at https://simpleaf.readthedocs.io/en/latest/ and tutorials forsimpleafthat have been developed can be accessed at https://combine-lab.github.io/alevin-fry-tutorials.