CAGEr
This package is for version 3.9 of Bioconductor; for the stable, up-to-date 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: 3.9
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 <charles.plessy at oist.jp>
citation("CAGEr")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CAGEr")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CAGEr")| CAGEr: an R package for CAGE data analysis and promoterome mining | HTML | R Script |
| Use of CAGE resources with CAGEr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | GPL-3 |
| Depends | methods, R (>= 2.15.0) |
| Imports | beanplot, BiocGenerics, BiocParallel, BSgenome, data.table, DelayedArray, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges(>= 1.23.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.5.27), KernSmooth, memoise, MultiAssayExperiment, plyr, Rsamtools, reshape, rtracklayer, S4Vectors, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | seqPattern |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | CAGEr_1.26.0.tar.gz |
| Windows Binary | CAGEr_1.26.0.zip |
| Mac OS X 10.11 (El Capitan) | CAGEr_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/CAGEr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CAGEr |
| Bioc Package Browser | https://code.bioconductor.org/browse/CAGEr/ |
| Package Short Url | https://bioconductor.org/packages/CAGEr/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |