ChIPseeker pipeline

ChIPseeker specifications


Unique identifier OMICS_07711
Name ChIPseeker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.2.5
Stability Stable
Maintained Yes


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  • person_outline Guangchuang Yu <>

Publication for ChIPseeker

ChIPseeker IN pipelines

PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] [11]., genome-wide peak coverage analysis and average occupancy profile for nf90/nf110 chip-seq data was performed in r with the chipseeker package and deeptools [74, 75]. motif enrichment analysis and gene annotation of nf90/nf110 chip-seq peaks were computed using hypergeometric optimization of motif enrichment (homer) [76]. […]

PMCID: 5886697
PMID: 29579120
DOI: 10.1371/journal.ppat.1006954

[…] bedtools [55] and ocrs were determined from these bed files using f-seq with default parameters [56]. no filtering of ocrs was performed. assignment of ocrs to gene promoters was performed using chipseeker [57]. 5kb docr length for each gene was calculated as the number of nucleotides in the 5kb directly downstream of the gene 3’ end that overlap an ocr. docr length for a gene was calculated […]

PMCID: 5527284
PMID: 28737171
DOI: 10.1038/ncomms16034

[…] s (version 2.17.0). bigwig files were generated using an enhanced perl script (courtesy of dr jim hughes, weatherhall institute of molecular medicine, university of oxford, uk). plots were made using chipseeker r/bioconductor package48., after primary chip, specific immunoprecipitates were washed, eluted, incubated with 10 mm dithiothreitol at 37 °c for 30 min, diluted 10 times in chip buffer (10  […]

PMCID: 4820141
PMID: 27042856
DOI: 10.1371/journal.pone.0152918

[…] a population) by bedtools version 2.22.1 [13]. these histone modifications were annotated in terms of closest genes and distances to transcriptional start sites (tss) of the genes by the package of chipseeker [14] in r version 3.1.0 when they were found in ≥85% (22 out of 26) among the lung adenocarcinoma cell lines. we focused on genes with the histone modification in their promoters defined […]

PMCID: 5133369
PMID: 27857068
DOI: 10.1038/emm.2016.101

[…] on the hiseq 2500 following the manufacturer's recommended protocol. after read trimming, bowtie v1.1.1 (read mapping), picard v1.133 (remove duplicates), macs 2 v2.1.0.20150420 (peak calling) and chipseeker (peak annotation) were used for downstream analysis., our synthetic scfv library was constructed using degenerate primers that yielded artificial sequences of hcdr3 on the backbone […]

ChIPseeker institution(s)
Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China; State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, China; Guangdong Information Center, Guangzhou, China

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