CAGEr

DOI: 10.18129/B9.bioc.CAGEr    

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

Bioconductor version: Release (3.6)

Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Author: Vanja Haberle <vanja.haberle at gmail.com>

Maintainer: Vanja Haberle <vanja.haberle at gmail.com>, Charles Plessy <plessy at riken.jp>

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	1.20.0
In Bioconductor since	BioC 2.12 (R-3.0) (5 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.

Source Package	CAGEr_1.20.0.tar.gz
Windows Binary	CAGEr_1.20.0.zip
Mac OS X 10.11 (El Capitan)	CAGEr_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CAGEr
Package Short Url	http://bioconductor.org/packages/CAGEr/
Package Downloads Report	Download Stats