source("http://bioconductor.org/biocLite.R")
biocLite("CAGEr")

CAGEr

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

Bioconductor version: 2.13

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 bio.uib.no>

Maintainer: Vanja Haberle <vanja.haberle at bio.uib.no>

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	1.4.1
In Bioconductor since	BioC 2.12 (R-3.0)
License	GPL-3
Depends	methods, R (>= 2.15.0), BSgenome, BSgenome.Mmusculus.UCSC.mm9
Imports	Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM
Suggests	BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, 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_1.4.1.tar.gz
Windows Binary	CAGEr_1.4.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	CAGEr_1.4.1.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats