To install this package, start R and enter:
source("http://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: 3.0
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:
source("http://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, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 1.10.3 |
| In Bioconductor since | BioC 2.12 (R-3.0) |
| License | GPL-3 |
| Depends | methods, R (>= 2.15.0), BSgenome |
| Imports | utils, Rsamtools, GenomicRanges, IRanges, data.table, beanplot, rtracklayer, som, VGAM |
| LinkingTo | |
| Suggests | BSgenome.Drerio.UCSC.danRer7, FANTOM3and4CAGE |
| SystemRequirements | |
| Enhances | parallel |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | CAGEr_1.10.3.tar.gz |
| Windows Binary | CAGEr_1.10.3.zip |
| Mac OS X 10.6 (Snow Leopard) | CAGEr_1.10.3.tgz |
| Mac OS X 10.9 (Mavericks) | CAGEr_1.10.3.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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