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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


No version available

Documentation


Maintainer


  • person_outline Guangchuang Yu

Publication for ChIPseeker

ChIPseeker citations

 (42)
library_books

The novel 19q13 KRAB zinc finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β catenin signalling

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

[…] xpression 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,. […]

library_books

Heterochromatin protects retinal pigment epithelium cells from oxidative damage by silencing p53 target genes

2018
Proc Natl Acad Sci U S A
PMCID: 5924883
PMID: 29622681
DOI: 10.1073/pnas.1715237115

[…] genome 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. […]

library_books

Enhancer variants reveal a conserved transcription factor network governed by PU.1 during osteoclast differentiation

2018
PMCID: 5874256
PMID: 29619268
DOI: 10.1038/s41413-018-0011-1

[…] calling, 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 in th […]

library_books

NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells

2018
PLoS One
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) []. NF90/N […]

library_books

Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

2018
Genome Biol
PMCID: 5872397
PMID: 29587824
DOI: 10.1186/s13059-018-1420-6

[…] ntified 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 at enha […]

library_books

HSV 1 induced disruption of transcription termination resembles a cellular stress response but selectively increases chromatin accessibility downstream of genes

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

[…] at 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 as […]

Citations

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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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