CAGEr

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

Bioconductor version: Release (2.14)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("CAGEr")

Documentation

PDF R Script CAGEr
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.6.0
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 Downloads

Package Source CAGEr_1.6.0.tar.gz
Windows Binary CAGEr_1.6.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) CAGEr_1.6.0.tgz
Mac OS X 10.9 (Mavericks)
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