cfTools:一个R/Bioconductor包,用于通过甲基化分析反卷积无细胞DNA。

IF 2.8 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Bioinformatics advances Pub Date : 2025-05-06 eCollection Date: 2025-01-01 DOI:10.1093/bioadv/vbaf108
Ran Hu, Shuo Li, Mary L Stackpole, Qingjiao Li, Xianghong Jasmine Zhou, Wenyuan Li
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引用次数: 0

摘要

动机:来自受损或病变组织的死亡细胞释放的无细胞DNA (cfDNA)可导致组织特异性DNA升高,这是可追溯的,并可通过独特的DNA甲基化模式进行量化。因此,通过分析其甲基化谱来追踪cfDNA的起源对于检测和监测包括癌症在内的一系列疾病具有巨大的潜力。然而,由于缺乏专门的、用户友好的生物信息学工具,反卷积组织特异性cfDNA在更广泛的应用和研究中仍然具有挑战性。结果:为了解决这个问题,我们开发了cfTools,这是一个R包,可以简化cfDNA组织起源分析,用于疾病检测和监测。cfTools集成了先进的cfDNA组织反褶积算法和R/Bioconductor兼容性,提供数据准备和分析功能,参数灵活,用户友好。通过识别异常的cfDNA组成,cfTools可以推断潜在病理状况的存在,包括但不限于癌症。它简化了生物信息学任务,使没有高级专业知识的用户能够轻松地从标准预处理的测序数据中获得生物学可解释的见解,从而增加了其可及性并扩大了其在基于cfdna的疾病研究中的应用。获取方法和实现方式:cfTools及其补充包cfToolsData可在Bioconductor: https://bioconductor.org/packages/release/bioc/html/cfTools.html和https://bioconductor.org/packages/release/data/experiment/html/cfToolsData.html免费获取。cfTools的开发版本维护在GitHub上:https://github.com/jasminezhoulab/cfTools。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
cfTools: an R/Bioconductor package for deconvolving cell-free DNA via methylation analysis.

Motivation: Cell-free DNA (cfDNA) released by dying cells from damaged or diseased tissues can lead to elevated tissue-specific DNA, which is traceable and quantifiable through unique DNA methylation patterns. Therefore, tracing cfDNA origins by analyzing its methylation profiles holds great potential for detecting and monitoring a range of diseases, including cancers. However, deconvolving tissue-specific cfDNA remains challenging for broader applications and research due to the scarcity of specialized, user-friendly bioinformatics tools.

Results: To address this, we developed cfTools, an R package that streamlines cfDNA tissue-of-origin analysis for disease detection and monitoring. Integrating advanced cfDNA tissue deconvolution algorithms with R/Bioconductor compatibility, cfTools offers data preparation and analysis functions with flexible parameters for user-friendliness. By identifying abnormal cfDNA compositions, cfTools can infer the presence of underlying pathological conditions, including but not limited to cancer. It simplifies bioinformatics tasks and enables users without advanced expertise to easily derive biologically interpretable insights from standard preprocessed sequencing data, thus increasing its accessibility and broadening its application in cfDNA-based disease studies.

Availability and implementation: cfTools and its supplementary package cfToolsData are freely available at Bioconductor: https://bioconductor.org/packages/release/bioc/html/cfTools.html and https://bioconductor.org/packages/release/data/experiment/html/cfToolsData.html. The development version of cfTools is maintained on GitHub: https://github.com/jasminezhoulab/cfTools.

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