ChIPseeker
This is the development version of ChIPseeker; for the stable release version, see ChIPseeker.
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Bioconductor version: Development (3.24)
This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.
Author: Guangchuang Yu [aut, cre]
, Ming Li [ctb], Qianwen Wang [ctb], Yun Yan [ctb], Hervé Pagès [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb], Zhougeng Xu [ctb], Chun-Hui Gao [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("ChIPseeker")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ChIPseeker")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPseeker")| ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, ChIPSeq, MultipleComparison, Software, Visualization |
| Version | 1.49.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | AnnotationDbi, aplot, BiocGenerics, boot, dplyr, enrichplot, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, graphics, grDevices, gtools, magrittr, methods, plotrix, parallel, RColorBrewer, rlang, rtracklayer, S4Vectors, scales, stats, tibble, TxDb.Hsapiens.UCSC.hg19.knownGene, utils, yulab.utils (>= 0.2.0) |
| System Requirements | |
| URL | https://yulab-smu.top/contribution-knowledge-mining/ |
| Bug Reports | https://github.com/YuLab-SMU/ChIPseeker/issues |
See More
| Suggests | clusterProfiler, ggimage, ggplotify, ggupset, ggVennDiagram, knitr, org.Hs.eg.db, prettydoc, ReactomePA, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg38.knownGene |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | EpiCompare, epiRomics, esATAC, segmenter |
| Suggests Me | GRaNIE, curatedAdipoChIP, cinaR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPseeker_1.49.0.tar.gz |
| Windows Binary (x86_64) | ChIPseeker_1.49.0.zip |
| macOS Binary (big-sur-x86_64) | ChIPseeker_1.49.0.tgz |
| macOS Binary (sonoma-arm64) | ChIPseeker_1.49.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPseeker |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ChIPseeker |
| Bioc Package Browser | https://code.bioconductor.org/browse/ChIPseeker/ |
| Package Short Url | https://bioconductor.org/packages/ChIPseeker/ |
| Package Downloads Report | Download Stats |