To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEr")

In most cases, you don't need to download the package archive at all.

CAGEr

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see CAGEr.

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Bioconductor version: 3.0

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:// URLs are not supported
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")
PDF R Script CAGEr
PDF Reference Manual
Text NEWS

Details

biocViews Clustering, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.10.3
In Bioconductor since BioC 2.12 (R-3.0) (3 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
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source CAGEr_1.10.3.tar.gz
Windows Binary CAGEr_1.10.3.zip
Mac OS X 10.6 (Snow Leopard) CAGEr_1.10.3.tgz
Mac OS X 10.9 (Mavericks) CAGEr_1.10.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CAGEr/tree/release-3.0
Package Short Url http://bioconductor.org/packages/CAGEr/
Package Downloads Report Download Stats

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