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chevron_left Topology enrichment analysis ChIP-seq data visualization Peak calling Tag density plot visualization Peak annotation chevron_right
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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

Versioning


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Documentation


Maintainer


  • person_outline Guangchuang Yu <>

Publication for ChIPseeker

ChIPseeker in pipelines

 (15)
2018
PMCID: 5873942
PMID: 29590119
DOI: 10.1371/journal.pone.0193126

[…] []., 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 [, ]. motif enrichment analysis and gene annotation of nf90/nf110 chip-seq peaks were computed using hypergeometric optimization of motif enrichment (homer) []. […]

2018
PMCID: 5886697
PMID: 29579120
DOI: 10.1371/journal.ppat.1006954

[…] using bedtools [] and ocrs were determined from these bed files using f-seq with default parameters []. no filtering of ocrs was performed. assignment of ocrs to gene promoters was performed using chipseeker []. 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 […]

2018
PMCID: 5924883
PMID: 29622681
DOI: 10.1073/pnas.1715237115

[…] were extracted using samtools version 0.1.18 (sourceforge). the peaks were called using a model-based analysis of chip-seq (macs14) (), with p < 10−5 as a threshold. peaks were annotated with chipseeker (). raw data have been submitted to the national center for biotechnology information’s sequence read archive database (https://www.ncbi.nlm.nih.gov/sra) under accession no. srp132687., ip […]

2018
PMCID: 5951945
PMID: 29760376
DOI: 10.1038/s41419-018-0604-z

[…] omnibus (geo, https://www.ncbi.nlm.nih.gov/geo) database. the gsm2424064_encff191ycr_fold_change_over_control_grch38.bigwig file was downloaded. we annotated those peaks by using r package “chipseeker”. subsequently, the gene region were intercepted with bedtools and exported to integrated genomics viewer software to map the peaks,., the function enrichments of differentially expressed […]

2017
PMCID: 5419091
PMID: 28453502
DOI: 10.12659/MSM.901191

[…] shocked for 10 and 20 min compared with the control samples, and recorded as peek-10 and peek-20, respectively. the threshold was p<10−5 and the default ultrasonic interrupt length was 300 bp. chipseeker was an r package for annotating chip-seq data analysis []. here, based on the chipseeker package, their related genes, distance to the closest transcription start sites (tss), and genome […]


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ChIPseeker in publications

 (35)
PMCID: 5951944
PMID: 29760402
DOI: 10.1038/s41598-018-25748-3

[…] and decreased tss groups by their fold-change values. calculations of distances from identified tsss to known promoters and genomic feature annotations were performed using the bioconductor package, chipseeker, version 1.6.7 with txdb.mmusculus.ucsc.mm10.knowngene, version 3.2.2., statistical analyses were performed using student’s t-test for comparisons between two groups, and dunnett’s test […]

PMCID: 5951945
PMID: 29760376
DOI: 10.1038/s41419-018-0604-z

[…] omnibus (geo, https://www.ncbi.nlm.nih.gov/geo) database. the gsm2424064_encff191ycr_fold_change_over_control_grch38.bigwig file was downloaded. we annotated those peaks by using r package “chipseeker”. subsequently, the gene region were intercepted with bedtools and exported to integrated genomics viewer software to map the peaks,., the function enrichments of differentially expressed […]

PMCID: 5874256
PMID: 29619268
DOI: 10.1038/s41413-018-0011-1

[…] motif analysis, and identification of superenhancers were done with homer software. global annotation of peaks with respect to tss and gene body was performed with the r bioconductor package chipseeker. centered k-means clustering was performed using cluster 3.0 and visualized using java-treeview program. over layered chip-seq peaks at noted loci were visualized using genome browser […]

PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] using sicer-diff at fdr < 0.01. unique and common differentially enriched peaks across all glioma stem-cell lines vs neural stem-cell lines were identified with bedops v2.4.20. the r package “chipseeker” was used to annotate chip peaks with general genomic features and compare feature distribution across different subsets of peaks. tag density plots of transcript abundance centered […]

PMCID: 5863514
PMID: 29599703
DOI: 10.3389/fnins.2018.00119

[…] or wiggletools (zerbino et al., ) gave a value of 0.9. peaks were annotated based on nearest transcription start site (tss) using the bioconductor package chippeakanno (zhu et al., ) and chipseeker (yu et al., ) and visualized using the gviz package (hahne and ivanek, )., the sp8 chipseq data presented in the “results” section were obtained using the goat polyclonal anti-sp8 […]


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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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