Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
Author
Abstract
Suggested Citation
DOI: 10.1371/journal.pcbi.1003326
Download full text from publisher
References listed on IDEAS
- Elizabeth G Wilbanks & Marc T Facciotti, 2010. "Evaluation of Algorithm Performance in ChIP-Seq Peak Detection," PLOS ONE, Public Library of Science, vol. 5(7), pages 1-12, July.
- Diaz Aaron & Park Kiyoub & Lim Daniel A. & Song Jun S., 2012. "Normalization, bias correction, and peak calling for ChIP-seq," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(3), pages 1-31, March.
Citations
Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
Cited by:
- Liang-Yu Fu & Tao Zhu & Xinkai Zhou & Ranran Yu & Zhaohui He & Peijing Zhang & Zhigui Wu & Ming Chen & Kerstin Kaufmann & Dijun Chen, 2022. "ChIP-Hub provides an integrative platform for exploring plant regulome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
- Pedro Madrigal & Siwei Deng & Yuliang Feng & Stefania Militi & Kim Jee Goh & Reshma Nibhani & Rodrigo Grandy & Anna Osnato & Daniel Ortmann & Stephanie Brown & Siim Pauklin, 2023. "Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
- Renata Bordeira-Carriço & Joana Teixeira & Marta Duque & Mafalda Galhardo & Diogo Ribeiro & Rafael D. Acemel & Panos. N. Firbas & Juan J. Tena & Ana Eufrásio & Joana Marques & Fábio J. Ferreira & Telm, 2022. "Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
- Shigekazu Murakami & Shannon M. White & Alec T. McIntosh & Chan D. K. Nguyen & Chunling Yi, 2023. "Spontaneously evolved progenitor niches escape Yap oncogene addiction in advanced pancreatic ductal adenocarcinomas," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
Most related items
These are the items that most often cite the same works as this one and are cited by the same works as this one.- Caiyan Jia & Matthew B Carson & Yang Wang & Youfang Lin & Hui Lu, 2014. "A New Exhaustive Method and Strategy for Finding Motifs in ChIP-Enriched Regions," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-13, January.
- Anthony Mathelier & Wyeth W Wasserman, 2013. "The Next Generation of Transcription Factor Binding Site Prediction," PLOS Computational Biology, Public Library of Science, vol. 9(9), pages 1-18, September.
- Weronika Sikora-Wohlfeld & Marit Ackermann & Eleni G Christodoulou & Kalaimathy Singaravelu & Andreas Beyer, 2013. "Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(11), pages 1-11, November.
- Yuzhuo Wang & Chengzhi Zhang & Kai Li, 2022. "A review on method entities in the academic literature: extraction, evaluation, and application," Scientometrics, Springer;Akadémiai Kiadó, vol. 127(5), pages 2479-2520, May.
- Dongjun Chung & Dan Park & Kevin Myers & Jeffrey Grass & Patricia Kiley & Robert Landick & Sündüz Keleş, 2013. "dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data," PLOS Computational Biology, Public Library of Science, vol. 9(10), pages 1-13, October.
- Apratim Mitra & Jiuzhou Song, 2012. "WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-11, September.
- Haipeng Xing & Yifan Mo & Will Liao & Michael Q Zhang, 2012. "Genome-Wide Localization of Protein-DNA Binding and Histone Modification by a Bayesian Change-Point Method with ChIP-seq Data," PLOS Computational Biology, Public Library of Science, vol. 8(7), pages 1-12, July.
- Tatsunori B Hashimoto & Matthew D Edwards & David K Gifford, 2014. "Universal Count Correction for High-Throughput Sequencing," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-11, March.
Corrections
All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pcbi00:1003326. See general information about how to correct material in RePEc.
If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.
If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .
If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.
For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: ploscompbiol (email available below). General contact details of provider: https://journals.plos.org/ploscompbiol/ .
Please note that corrections may take a couple of weeks to filter through the various RePEc services.