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CENTIPEDE specifications


Unique identifier OMICS_11375
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


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  • person_outline Jacob Degner <>

Publication for CENTIPEDE

CENTIPEDE citations


Global dynamics of stage specific transcription factor binding during thymocyte development

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 […]


Computational Methods for Assessing Chromatin Hierarchy

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 [,]. […]


Genome wide prediction of DNase I hypersensitivity using gene expression

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 […]


Differential chromatin profiles partially determine transcription factor binding

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 […]


Layer specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

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 […]


Genome scale high resolution mapping of activating and repressive nucleotides in regulatory regions

PMCID: 5125825
PMID: 27701403
DOI: 10.1038/nbt.3678

[…] inferences, including dnase-based,,,, and dnase-independent predictions of tf-bound nucleotides, and both motif-based,, and motif independent,, predictions of regulatory nucleotides. for example, centipede motif annotations showed strong agreement for both activating and repressive scores at the nucleotide level (, left, ), at the region level (, ), and for specific regulators (), […]

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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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