PeakAnalyzer protocols

PeakAnalyzer specifications

Information


Unique identifier OMICS_02156
Name PeakAnalyzer
Software type Toolkit/Suite
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A single peak file and a feature annotation file.
Input format BED+WIG,BED,GTF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Java
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • PeakAnnotator
  • PeakSplitter

Versioning


Add your version

Maintainers


  • person_outline Mali Salmon-Divon <>
  • person_outline Paul Bertone <>

Additional information


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

Publication for PeakAnalyzer

PeakAnalyzer IN pipelines

 (2)
2016
PMCID: 4891180
PMID: 27178982
DOI: 10.7554/eLife.12717.044

[…] by sampling the number of genes represented in the microarray 1000 times and assuming a normal distribution. annotation of binding events and association with genomic features was performed with peakanalyzer (salmon-divon et al., 2010) and the r/bioconductor package chippeakanno (zhu et al., 2010)., postnatal brains collected at p7 and p15 were fixed by immersion in 4% paraformaldehyde […]

2011
PMCID: 3273378
PMID: 22139358
DOI: 10.1038/emboj.2011.431

[…] used for each comparison, and regions that were determined to be significantly enriched by both peak callers were included in downstream analyses. annotation of modified regions was performed with peakanalyzer (salmon-divon et al, 2010) and ceas (shin et al, 2009)., the refseq gene model annotation was used to define transcription start and end sites. the ceas tool (shin et al, 2009) was used […]

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

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