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 is the development version of CAGEr; for the stable 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: Development (3.4)

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, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.15.0
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(>= 1.23.16), IRanges(>= 2.5.27), 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_1.15.0.tar.gz
Windows Binary CAGEr_1.15.0.zip
Mac OS X 10.9 (Mavericks) CAGEr_1.15.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/CAGEr
Package Short Url http://bioconductor.org/packages/CAGEr/
Package Downloads Report Download Stats

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