The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
Abstract
Summary: 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. Availability and implementation: 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). Contact: guangchuangyu@gmail.com or tqyhe@jnu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters
Yu, G., Wang, L.-G., Han, Y., & He, Q.-Y. (2012) · OMICS: A Journal of Integrative Biology · doi:10.1089/omi.2011.0118 · Cited by 36,259
Self-citation
Research works printed but not linked: 8
- Gentleman, 2004, Bioconductor: open software development for computational biology and bioinformatics, Genome Biol., 5, R80, 10.1186/gb-2004-5-10-r80 · DOI · Paper page
- Huang, 2013, PAVIS: a tool for peak annotation and visualization, Bioinformatics, 29, 3097, 10.1093/bioinformatics/btt520 · DOI
- Lawrence, 2013, Software for computing and annotating genomic ranges, PLoS Comput. Biol., 9, e1003118, 10.1371/journal.pcbi.1003118 · DOI · Paper page
- Perez-Pinera, 2013, Synergistic and tunable human gene activation by combinations of synthetic transcription factors, Nat. Methods, 10, 239, 10.1038/nmeth.2361 · DOI · Paper page
- Salmon-Divon, 2010, PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci, BMC Bioinformatics, 11, 415, 10.1186/1471-2105-11-415 · DOI · Paper page
- Yu, 2015, DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis, Bioinformatics, 31, 608, 10.1093/bioinformatics/btu684 · DOI · Paper page
- Zhu, 2008, Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks, Nat. Genet., 40, 854, 10.1038/ng.167 · DOI · Paper page
- Zhu, 2010, ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data, BMC Bioinformatics, 11, 237, 10.1186/1471-2105-11-237 · DOI · Paper page
Cited by
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
(2021) · doi:10.1016/j.xinn.2021.100141 · Cited by 12,455
ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
Yu, G., & He, Q.-Y. (2015) · Molecular BioSystems · doi:10.1039/c5mb00663e · Cited by 1,918
Self-citationSiddiqui, I., Schaeuble, K., Chennupati, V., Fuertes Marraco, S. A., Calderon-Copete, S., Pais Ferreira, D., Carmona, S. J., Scarpellino, L., Gfeller, D., Pradervand, S., et al. (2019) · Immunity · doi:10.1016/j.immuni.2018.12.021 · Cited by 1,679
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain
Lake, B. B., Chen, S., Sos, B. C., Fan, J., Kaeser, G. E., Yung, Y. C., Duong, T. E., Gao, D., Chun, J., Kharchenko, P. V., et al. (2018) · Nature Biotechnology · doi:10.1038/nbt.4038 · Cited by 983
Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade
Ishizuka, J. J., Manguso, R. T., Cheruiyot, C. K., Bi, K., Panda, A., Iracheta-Vellve, A., Miller, B. C., Du, P. P., Yates, K. B., Dubrot, J., et al. (2019) · Nature · doi:10.1038/s41586-018-0768-9 · Cited by 697
Metadata
- Authors
- Yu, G., Wang, L.-G., & He, Q.-Y.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-03-11
- Volume
- 31
- Issue
- 14
- Pages
- 2382-2383
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2170830174
- Cited by
- 4,362
- References
- 1
- FWCI
- 21.74
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. https://app.cochat.ai/papers/10.1093/bioinformatics/btv145
- The paper
- Yu, G., Wang, L.-G., & He, Q.-Y. (2015). ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv145
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
