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PeakAnnotator specifications

Information


Unique identifier OMICS_23188
Name PeakAnnotator
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainers


  • person_outline Mali Salmon-Divon
  • person_outline Paul Bertone

Additional information


https://www.ebi.ac.uk/research/bertone/software

Publication for PeakAnnotator

PeakAnnotator citations

 (4)
call_split

Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer

2017
Oncotarget
PMCID: 5400527
PMID: 28411283
DOI: 10.18632/oncotarget.16244
call_split See protocol

[…] h allows for a sensitive and robust prediction of peaks. The IGV browser [] was used to visually check called peaks and produce the ChIP-Seq traces in Figure and . Peaks were assigned to genes using PeakAnnotator in the PeakAnalyzer package where positive genes were determined by the presence of a peak in a -2kb and +2.5Kb window around the transcription start site (TSS) []. The Venn diagrams of […]

library_books

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

2016
Oncotarget
PMCID: 5041931
PMID: 27016420
DOI: 10.18632/oncotarget.8239

[…] e-end reads. The sequencing reads were also aligned to the reference sequence (hg 19) using the BWA software. The results generated by MACS (v.1.4.2) [] were loaded into the IGV for visualization []. PeakAnnotator from Homer (v 4.7) was used to annotate each peak. All ChIP sequencing data were deposited in the public repository (GEO Accession Number: GSE75595). Bam files were available at http://m […]

library_books

Pharmacological targeting of the Wdr5 MLL interaction in C/EBPα N terminal leukemia

2015
Nat Chem Biol
PMCID: 4511833
PMID: 26167872
DOI: 10.1038/nchembio.1859

[…] resulting peak lists were annotated with regard to transcription start sites using the Bioconductor package ChIPpeakAnno (http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html) and PeakAnnotator and post-processed with custom R scripts utilizing the ggplot2 plotting system (http://ggplot2.org/). […]

library_books

A Comprehensive Functional Portrait of Two Heat Shock Factor Type Transcriptional Regulators Involved in Candida albicans Morphogenesis and Virulence

2013
PLoS Pathog
PMCID: 3744398
PMID: 23966855
DOI: 10.1371/journal.ppat.1003519

[…] g the Galaxy tool Intercept version 1.0.0 (https://main.g2.bx.psu.edu/). The complete Sfl1p and Sfl2p binding and expression datasets are provided in Tables S1–S8 in . The command line version of the PeakAnnotator (v 1.4) sub-package from the PeakAnalyzer suite of algorithms was used to annotate the Sfl1p and Sfl2p binding peaks in Tables S1, S2, S4 and S5 in . The association of peaks to target […]

Citations

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PeakAnnotator institution(s)
EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
PeakAnnotator funding source(s)
Supported by from EMBL and BBSRC grant BBG0156781.

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