CENTIPEDE protocols

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CENTIPEDE specifications

Information


Unique identifier OMICS_11375
Name CENTIPEDE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Jacob Degner <>

Publication for CENTIPEDE

CENTIPEDE in pipeline

2015
PMCID: 4514710
PMID: 26208222
DOI: 10.1371/journal.pone.0133280

[…] several methods for prediction of tf binding using dgf have been described in different cell-types from yeast to human [–,–]. different computational prediction tools such as wellington [], centipede [], dnase2tf [] and footprint detection software [] are available. we have devised an approach that uses dgf datasets from [], in combination with motiflab [] and four c-myb motifs […]


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CENTIPEDE in publications

 (18)
PMCID: 5884796
PMID: 29618724
DOI: 10.1038/s41598-018-23774-9

[…] in the open chromatin landscape across thymocyte maturation., in order to achieve greater insights into genomic dna sequences that are bound by tfs, we performed tf footprinting predictions using centipede. to validate the performance of centipede footprint calls in our thymocyte data, we first compared our results with gata3 chip-seq data in dn and dp thymocytes (gse20898) and ctcf chip-seq […]

PMCID: 5910504
PMID: 29686798
DOI: 10.1016/j.csbj.2018.02.003

[…] tools, dnase2tf [] offers better detection accuracy and requires less computing time. in the analysis of atac-seq data, the positions of both nucleosome and tf-binding chromatin are identified using centipede []. as algorithms exhibit various sensitivities and specificities, it is beneficial to analyze data using more than one tool because discrepancies in peak calling have been reported [,]. […]

PMCID: 5715040
PMID: 29051481
DOI: 10.1038/s41467-017-01188-x

[…] turned out to be smaller than the differences between prediction methods (fig. ; supplementary figs. –). we also compared our methods with two state-of-the-art tfbs prediction methods piq and centipede. both piq and centipede use true dnase-seq data and motif information to make predictions. piq showed comparable performance with our true dnase-seq method, whereas centipede performed […]

PMCID: 5509100
PMID: 28704389
DOI: 10.1371/journal.pone.0179411

[…] factor binding in different conditions has not been comprehensively studied., several methods have been developed to infer transcription factor binding from chromatin accessibility data. centipede [] uses a bayesian hierarchical model for dnase data to infer bound and unbound sites. piq [] uses a discriminative model to detect bound sites from unbound sites. the key feature […]

PMCID: 5325622
PMID: 28112643
DOI: 10.7554/eLife.21883.061

[…] (flagstat). we used collectinsertsizemetrics.jar from picard v1.110 (rrid:scr_006525) () to analyze fragment size statistics, and preseq v0.1.0 () to analyze library sequencing saturation. the centipede package for r () was used to analyze insertions near atf2 motif locations obtained from the swissregulon database (rrid:scr_005333) (, ). to downsample bam files, the data were sorted […]


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CENTIPEDE institution(s)
Department of Human Genetics, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA; Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
CENTIPEDE funding source(s)
This work was supported by grants from the National Institutes of Health, by the Howard Hughes Medical Institute, by the Chicago Fellows Program, by the American Heart Association, and by the NIH Genetics and Regulation Training grant.

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