CAGEr
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Bioconductor version: Release (2.12)
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
| R Script | CAGEr | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Clustering, HighThroughputSequencing, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 1.2.9 |
| In Bioconductor since | BioC 2.13 (R-2.18) |
| 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_1.2.9.tar.gz |
| Windows Binary | CAGEr_1.2.9.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | CAGEr_1.2.9.tgz |
| Package Downloads Report | Download Stats |
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