TY - JOUR
T1 - CpGtools
T2 - a python package for DNA methylation analysis
AU - Wei, Ting
AU - Nie, Jinfu
AU - Larson, Nicholas B.
AU - Ye, Zhenqing
AU - Eckel-Passow, Jeanette E.
AU - Robertson, Keith D.
AU - Kocher, Jean Pierre A.
AU - Wang, Liguo
N1 - Publisher Copyright:
© The Author(s) 2019. Published by Oxford University Press. All rights reserved.
PY - 2021/6/1
Y1 - 2021/6/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85112124521&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85112124521&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btz916
DO - 10.1093/bioinformatics/btz916
M3 - Article
C2 - 31808791
AN - SCOPUS:85112124521
SN - 1367-4803
VL - 37
SP - 1598
EP - 1599
JO - Bioinformatics
JF - Bioinformatics
IS - 11
ER -