FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data

doi:10.1186/s12864-022-08506-8

	FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data
	Shang, Guan Dong 1,2; Xu, Zhou Geng 1,2; Wan, Mu Chun1,3 ; Wang, Fu Xiang 1,2; Wang, Jia Wei1,2,3
	2022-04-07
发表期刊	BMC GENOMICS (IF:3.5[JCR-2023],4.1[5-Year])
EISSN	1471-2164
卷号	23
发表状态	已发表
DOI	10.1186/s12864-022-08506-8
摘要	Background: Transcription factors (TFs) play central roles in regulating gene expression. With the rapid growth in the use of high-throughput sequencing methods, there is a need to develop a comprehensive data processing and analyzing framework for inferring influential TFs based on ChIP-seq/ATAC-seq datasets. Results: Here, we introduce FindIT2 (Find Influential TFs and Targets), an R/Bioconductor package for annotating and processing high-throughput multi-omics data. FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by the combination of ChIP-seq and RNA-seq datasets, and inferring influential TFs based on different types of data input. Moreover, benefited from the annotation framework based on Bioconductor, FindIT2 can be applied to any species with genomic annotations, which is particularly useful for the non-model species that are less well-studied. Conclusion: FindIT2 provides a user-friendly and flexible framework to generate results at different levels according to the richness of the annotation information of user’s species. FindIT2 is compatible with all the operating systems and is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (https://bioconductor.org/packages/devel/bioc/html/FindIT2.html).
关键词	ATAC-seq ChIP-seq Chromatin accessibility Gene regulation R package Transcription factor
URL	查看原文
收录类别	SCIE
语种	英语
Scopus 记录号	2-s2.0-85127932776
来源库	Scopus
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/176060
专题	生命科学与技术学院_特聘教授组_王佳伟组生命科学与技术学院_博士生
作者单位	1.National Key Laboratory of Plant Molecular Genetics (NKLPMG),CAS Center for Excellence in Molecular Plant Sciences,Institute of Plant Physiology and Ecology (SIPPE),Chinese Academy of Sciences (CAS),Shanghai,200032,China 2.University of Chinese Academy of Sciences (UCAS),Shanghai,200032,China 3.School of Life Science and Technology,ShanghaiTech University,Shanghai,201210,China
推荐引用方式 GB/T 7714	Shang, Guan Dong,Xu, Zhou Geng,Wan, Mu Chun,et al. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data[J]. BMC GENOMICS,2022,23.
APA	Shang, Guan Dong,Xu, Zhou Geng,Wan, Mu Chun,Wang, Fu Xiang,&Wang, Jia Wei.(2022).FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.BMC GENOMICS,23.
MLA	Shang, Guan Dong,et al."FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data".BMC GENOMICS 23(2022).