To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEr")

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CAGEr

DOI: 10.18129/B9.bioc.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 (3.7)

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>

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

HTML R Script CAGEr: an R package for CAGE data analysis and promoterome mining
PDF   Reference Manual
Text   NEWS

Details

biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 1.21.2
In Bioconductor since BioC 2.12 (R-3.0) (4.5 years)
License GPL-3
Depends methods, R (>= 2.15.0)
Imports beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, GenomeInfoDb, GenomicRanges(>= 1.23.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.5.27), KernSmooth, MultiAssayExperiment, plyr, Rsamtools, reshape, rtracklayer, S4Vectors, som, SummarizedExperiment, utils, vegan, VGAM
LinkingTo
Suggests BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
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_1.21.2.tar.gz
Windows Binary CAGEr_1.21.0.zip
Mac OS X 10.11 (El Capitan) CAGEr_1.21.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CAGEr
Package Short Url http://bioconductor.org/packages/CAGEr/
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