To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEr")
In most cases, you don't need to download the package archive at all.
CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Bioconductor version: 3.1
Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).
Author: Vanja Haberle, Department of Biology, University of Bergen, Norway <vanja.haberle at gmail.com>
Maintainer: Vanja Haberle <vanja.haberle at gmail.com>
Citation (from within R,
enter citation("CAGEr")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEr")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CAGEr")
| R Script | CAGEr | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 1.10.1 |
| In Bioconductor since | BioC 2.12 (R-3.0) (2.5 years) |
| License | GPL-3 |
| Depends | methods, R (>= 2.15.0), BSgenome |
| Imports | utils, Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM |
| LinkingTo | |
| Suggests | BSgenome.Drerio.UCSC.danRer7, FANTOM3and4CAGE |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | seqPattern |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CAGEr_1.10.1.tar.gz |
| Windows Binary | CAGEr_1.10.1.zip |
| Mac OS X 10.6 (Snow Leopard) | CAGEr_1.10.1.tgz |
| Mac OS X 10.9 (Mavericks) | CAGEr_1.10.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CAGEr/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/CAGEr/ |
| Package Downloads Report | Download Stats |
Documentation »
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