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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
In most cases, you don't need to download the package archive at all.
ChIPseeker
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
Bioconductor version: 3.0
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
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation (from within R,
enter citation("ChIPseeker")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("ChIPseeker")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ChIPseeker")
| 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 | 1.2.6 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.0) |
| Imports | BiocGenerics, AnnotationDbi, data.table, IRanges, GenomeInfoDb, GenomicRanges, GenomicFeatures, ggplot2, gplots, grDevices, gtools, methods, plotrix, plyr, RColorBrewer, rtracklayer, S4Vectors, TxDb.Hsapiens.UCSC.hg19.knownGene |
| LinkingTo | |
| Suggests | clusterProfiler, ReactomePA, DOSE, GOSemSim, org.Hs.eg.db, knitr |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/GuangchuangYu/ChIPseeker |
| Depends On Me | |
| Imports Me | |
| Suggests Me | DOSE, GOSemSim, ReactomePA |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ChIPseeker_1.2.6.tar.gz |
| Windows Binary | ChIPseeker_1.2.6.zip |
| Mac OS X 10.6 (Snow Leopard) | ChIPseeker_1.2.6.tgz |
| Mac OS X 10.9 (Mavericks) | ChIPseeker_1.2.6.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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