ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

Bioinformatics
Guangchuang YuQing-Yu He

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. 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).

References

Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
May 13, 2010·BMC Bioinformatics·Lihua J ZhuMichael R Green
Aug 10, 2010·BMC Bioinformatics·Mali Salmon-DivonPaul Bertone
Mar 30, 2012·Omics : a Journal of Integrative Biology·Guangchuang YuQing-Yu He
Feb 5, 2013·Nature Methods·Pablo Perez-PineraCharles A Gersbach
Aug 21, 2013·PLoS Computational Biology·Michael LawrenceVincent J Carey
Sep 7, 2013·Bioinformatics·Weichun HuangLeping Li

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Citations

Mar 17, 2016·Genomics Data·António Miguel de Jesus DominguesFederico Calegari
Dec 17, 2015·Cell Metabolism·Ida DonkinRomain Barrès
Dec 15, 2015·Molecular BioSystems·Guangchuang Yu, Qing-Yu He
Sep 14, 2015·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Margherita ScarpatoTeresa Capriglione
Aug 19, 2016·PLoS Computational Biology·Charles Joly BeauparlantArnaud Droit
Aug 27, 2016·Molecular Biology and Evolution·Isabel MendizabalSoojin V Yi
Nov 5, 2016·The Journal of Experimental Medicine·Zhenhua YangHao Jiang
Sep 23, 2016·Pathology Oncology Research : POR·Pengfei LiuHuilai Zhang
Jan 28, 2017·Epigenetics : Official Journal of the DNA Methylation Society·Ligia A PapaleReid S Alisch
Feb 22, 2017·ELife·Juliana S CapitanioRichard W Wozniak
Mar 28, 2017·Nature Structural & Molecular Biology·Beatrice BodegaValerio Orlando
Mar 23, 2017·Frontiers in Behavioral Neuroscience·Florian Duclot, Mohamed Kabbaj
Jan 21, 2017·American Journal of Respiratory Cell and Molecular Biology·David GozalAbdelnaby Khalyfa
May 16, 2017·Nature Genetics·Rita KhoueiryKian Peng Koh
Apr 28, 2017·Bioinformatics·Jens LichtenbergDavid M Bodine
Dec 8, 2017·The Journal of Experimental Medicine·Jason S WeinsteinJoe Craft
Nov 17, 2017·Nature·Tobias HirschMichele De Luca
Dec 30, 2017·Genome Biology·N BartonicekM E Dinger
May 24, 2018·Bioinformatics·Guangchuang Yu
Oct 14, 2017·Nuclear Receptor Research·Brandon PraslickaChris R Gissendanner

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