title: ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
abstract: ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among ChIP-seq datasets. Currently, ChIPseeker contains 15 000 bed file information from GEO database. These datasets can be downloaded and compare with user's own data to explore significant overlap datasets for inferring co-regulation or transcription factor complex for further investigation.
  
  
  METHODS
  ChIPseeker is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ChIPseeker.html).
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China, State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong SAR, China and.
authors.forename: Guangchuang
authors.initials: G
authors.lastname: Yu
authors.affiliation: Guangdong Information Center, Guangzhou 510031, China.
authors.forename: Li-Gen
authors.initials: LG
authors.lastname: Wang
authors.affiliation: Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
authors.forename: Qing-Yu
authors.initials: QY
authors.lastname: He
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D014157:Transcription Factors; D004247:DNA