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ChIPOTle specifications

Information


Unique identifier OMICS_00803
Name ChIPOTle
Alternative names Chromatin ImmunoPrecipitation On Tiled arrays, ChIPOTle Peak Finder, ChIPOTle 2.0 Peak Discrimination Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages C++, Perl
License Academic Free License version 3.0, GNU General Public License version 2.0
Computer skills Medium
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jason Lieb <>

Additional information


https://sourceforge.net/projects/chipotle-perl/

Publication for Chromatin ImmunoPrecipitation On Tiled arrays

ChIPOTle in publications

 (17)
PMCID: 4905549
PMID: 26896331
DOI: 10.1534/genetics.115.184218

[…] biological replicates. the data were normalized using the median correction method, and replicates were combined with ebayes from the r limma package (; ). significant peaks were identified using chipotle (). to detect potential promoter occupancy, the peak was considered only when within 1000 bp (the average length of the sonicated dna fragments) of the promoter region, defined as 0–1500 bp […]

PMCID: 4454661
PMID: 26039089
DOI: 10.1371/journal.pone.0127523

[…] data are associated with the dataset deposited in the geo data repository (www.ncbi.nlm.nih.gov/geo/) under accession number gse63715. in order to identify peaks, the microarray data was loaded onto chipotle visual basic for applications macro [] and then visualized in the integrated genome browser (igb) affymetrix (version 8.1.8), []. each chip-chip experiment for each strain was performed […]

PMCID: 3772097
PMID: 24068963
DOI: 10.1371/journal.pgen.1003798

[…] point were background subtracted so that the distributions centered over 0. the most repetitive probes (1.1%) were removed from analyses. orc binding regions (peaks) were determined with the program chipotle using a window size of 240 bp, a step size of 60 bp, and a p-value of 10−5 . the raw orc gemsa data has been deposited to gene expression omnibus (http://www.ncbi.nlm.nih.gov/geo), accession […]

PMCID: 3730917
PMID: 23695302
DOI: 10.1534/genetics.113.150870

[…] with a genepix4200a scanner (molecular devices, sunnyvale, ca), and the transcriptome and chip-chip data were normalized with the r bioconductor limma package. the chip-chip data were analyzed by chipotle peak finder excel macro (). cluster 3.0 () and java treeview 1.1.6r2 () were used to create heat-map images of microarray expression and chip-chip data. the microarray expression […]

PMCID: 3516552
PMID: 23236291
DOI: 10.1371/journal.pgen.1003104

[…] ca) except for the use of human cot-1 dna. the washing and scanning of the microarrays were performed as described above. the chip-chip data was normalized by scaling in limma and analyzed by chipotle peak finder excel macro with the default setting of log2 ratio cut-off of 1. peaks located within 3 kb upstream of a start codon and 2 kb downstream of a start codon within a coding region […]


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ChIPOTle institution(s)
Department of Biology and Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Statistics, University of North Carolina at Chapel Hill, Chapel Hill, USA
ChIPOTle funding source(s)
Supported by NIH grants (F32HG002989, R01GM072518) and by an NSF grant (DMS-0406361).

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