To install this package, start R and enter:

source("http://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: Release (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:

source("http://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 1.8.1
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-3
Depends methods, R (>= 2.15.0), BSgenome
Imports Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM
Suggests BSgenome.Drerio.UCSC.danRer7, FANTOM3and4CAGE
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source CAGEr_1.8.1.tar.gz
Windows Binary CAGEr_1.8.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CAGEr_1.8.1.tgz
Mac OS X 10.9 (Mavericks) CAGEr_1.8.1.tgz
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