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
|
|
|
|
|
|
|
|
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Bioconductor version: Release (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")
| R Script | CAGEr | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 1.16.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (4 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_1.16.0.tar.gz |
| Windows Binary | CAGEr_1.16.0.zip |
| Mac OS X 10.9 (Mavericks) | CAGEr_1.16.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/CAGEr/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/CAGEr/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
