PCBS：一个用于快速准确分析亚硫酸氢盐测序数据的 R 包。
PCBS: an R package for fast and accurate analysis of bisulfite sequencing data.
机构信息
The Razavi Newman Integrative Genomics and Bioinformatics Core Facility, The Salk Institute for Biological Studies, La Jolla, CA 92037, United States.
出版信息
Bioinformatics. 2024 Oct 1;40(10). doi: 10.1093/bioinformatics/btae593.
MOTIVATION
Whole-genome bisulfite sequencing is a powerful tool for analyzing chromatin methylation genome-wide, but analysis of whole-genome bisulfite data is slow, inflexible, and often inaccurate.
RESULTS
We developed PCBS (Principal Component BiSulfite), a computationally efficient R package for Whole Genome Bisulfite Sequencing analysis that demonstrates remarkable accuracy and flexibility compared to current tools. PCBS identifies differentially methylated loci, differentially methylated regions, and offers novel functionality that allows for more targeted methylation analyses. PCBS uses minimal computational resources; a complete pipeline in mouse can run on a local RStudio instance in a matter of minutes.
AVAILABILITY AND IMPLEMENTATION
PCBS is an R package available under a GNU GPLv3 license on GitHub: https://github.com/katlande/PCBS and CRAN: https://CRAN.R-project.org/package=PCBS. Instructions for use are available at: https://katlande.github.io/PCBS/.
动机
全基因组亚硫酸氢盐测序是一种强大的工具，可用于全面分析染色质甲基化，但全基因组亚硫酸氢盐数据的分析速度慢、不灵活，且常常不准确。
结果
我们开发了 PCBS（主成分双硫代修饰），这是一个用于全基因组亚硫酸氢盐测序分析的计算效率高的 R 包，与当前的工具相比，它具有显著的准确性和灵活性。PCBS 可识别差异甲基化基因座和差异甲基化区域，并提供新颖的功能，允许更有针对性的甲基化分析。PCBS 仅使用最小的计算资源；在本地 RStudio 实例上，整个小鼠的完整分析流程可以在几分钟内运行完毕。
可用性和实施
PCBS 是一个基于 GNU GPLv3 许可证的 R 包，可在 GitHub（https://github.com/katlande/PCBS）和 CRAN（https://CRAN.R-project.org/package=PCBS）上获得。使用说明可在以下网址获得：https://katlande.github.io/PCBS/。
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