ChIPseeker protocols

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ChIPseeker computational protocol

ChIPseeker specifications

Information


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 1.16.1
Stability Stable
Requirements
AnnotationDbi, methods, stats, RColorBrewer, gplots, parallel, grid, graphics, BiocGenerics, utils, testthat, GenomeInfoDb, rtracklayer, BiocStyle, grDevices, dplyr, gtools, rmarkdown, knitr, plotrix, gridBase, S4Vectors(>=0.17.25), IRanges(>=2.13.12), org.Hs.eg.db, GenomicRanges(>=1.31.8), TxDb.Hsapiens.UCSC.hg19.knownGene, magrittr, R(>=3.4.0), boot, GenomicFeatures(>=1.31.3), clusterProfiler, ggplot2(>=2.2.0), enrichplot, UpSetR, ReactomePA
Maintained Yes

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Documentation


Maintainer


  • person_outline Guangchuang Yu <>

Publication for ChIPseeker

ChIPseeker IN pipelines

 (5)
2018
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]. […]

2018
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 […]

2017
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  […]

2016
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 […]

2016
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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