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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
In most cases, you don't need to download the package archive at all.
ChIPseeker
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ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Bioconductor version: Release (3.5)
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], Yun Yan [ctb], Herve Pages [ctb], Michael Kluge [ctb], Thomas Schwarzl [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation (from within R,
enter citation("ChIPseeker")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
Documentation
| HTML | R Script | ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Annotation, ChIPSeq, MultipleComparison, Software, Visualization |
| Version | 1.12.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.2) |
| Imports | AnnotationDbi, BiocGenerics, boot, DOSE(>= 3.0.0), IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2 (>= 2.2.0), gplots, graphics, grDevices, grid, gridBase, gtools, methods, plotrix, dplyr, parallel, magrittr, RColorBrewer, rtracklayer, S4Vectors, stats, TxDb.Hsapiens.UCSC.hg19.knownGene, UpSetR, utils |
| LinkingTo | |
| Suggests | clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle, rmarkdown, testthat |
| SystemRequirements | |
| Enhances | |
| URL | https://guangchuangyu.github.io/ChIPseeker |
| BugReports | https://github.com/GuangchuangYu/ChIPseeker/issues |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ChIPseeker_1.12.1.tar.gz |
| Windows Binary | ChIPseeker_1.12.1.zip |
| Mac OS X 10.11 (El Capitan) | ChIPseeker_1.12.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ChIPseeker |
| Package Short Url | http://bioconductor.org/packages/ChIPseeker/ |
| Package Downloads Report | Download Stats |
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