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CpGtools: a python package for DNA methylation analysis

文献类型：期刊论文

作者Wei, Ting1; Nie, Jinfu2; Larson, Nicholas B.1; Ye, Zhenqing1; Eckel-Passow, Jeanette E.1; Robertson, Keith D.3; Kocher, Jean-Pierre A.1; Wang, Liguo1
刊名BIOINFORMATICS
出版日期2021-06-01
卷号37
ISSN号1367-4803
DOI10.1093/bioinformatics/btz916
通讯作者Kocher, Jean-Pierre A.(kocher.jeanpierre@mayo.edu) ; Wang, Liguo(Wang.Liguo@mayo.edu)
英文摘要Motivation: DNA methylation can be measured at the single CpG level using sodium bisulfite conversion of genomic DNA followed by sequencing or array hybridization. Many analytic tools have been developed, yet there is still a high demand for a comprehensive and multifaceted tool suite to analyze, annotate, QC and visualize the DNA methylation data. Results: We developed the CpGtools package to analyze DNA methylation data generated from bisulfite sequencing or Illumina methylation arrays. The CpGtools package consists of three types of modules: (i) 'CpG position modules' focus on analyzing the genomic positions of CpGs, including associating other genomic and epigenomic features to a given list of CpGs and generating the DNA motif logo enriched in the genomic contexts of a given list of CpGs; (ii) 'CpG signal modules' are designed to analyze DNA methylation values, such as performing the PCA or t-SNE analyses, using Bayesian Gaussian mixture modeling to classify CpG sites into fully methylated, partially methylated and unmethylated groups, profiling the average DNA methylation level over user-specified genomics regions and generating the bean/violin plots and (iii) 'differential CpG analysis modules' focus on identifying differentially methylated CpGs between groups using different statistical methods including Fisher's Exact Test, Student's t-test, ANOVA, non-parametric tests, linear regression, logistic regression, beta-binomial regression and Bayesian estimation.
资助项目NIH[R01CA224917] ; NIH[R01AA27179]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
语种英语
WOS记录号WOS:000703906200016
出版者OXFORD UNIV PRESS
资助机构NIH
源URL[http://ir.hfcas.ac.cn:8080/handle/334002/124930]  
专题中国科学院合肥物质科学研究院
通讯作者Kocher, Jean-Pierre A.; Wang, Liguo
作者单位1.Mayo Clin, Dept Hlth Sci Res, Div Biomed Stat & Informat, Rochester, MN 55905 USA
2.Chinese Acad Sci, Ctr Med Phys & Technol, Hefei Inst Phys Sci, Anhui Prov Key Lab Med Phys & Technol, Hefei 230031, Anhui, Peoples R China
3.Mayo Clin, Dept Mol Pharmacol & Expt Therapeut, Rochester, MN 55905 USA
推荐引用方式
GB/T 7714		 Wei, Ting,Nie, Jinfu,Larson, Nicholas B.,et al. CpGtools: a python package for DNA methylation analysis[J]. BIOINFORMATICS,2021,37.
APA Wei, Ting.,Nie, Jinfu.,Larson, Nicholas B..,Ye, Zhenqing.,Eckel-Passow, Jeanette E..,...&Wang, Liguo.(2021).CpGtools: a python package for DNA methylation analysis.BIOINFORMATICS,37.
MLA Wei, Ting,et al."CpGtools: a python package for DNA methylation analysis".BIOINFORMATICS 37(2021).

入库方式： OAI收割

来源：合肥物质科学研究院

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