CAGEr

DOI: 10.18129/B9.bioc.CAGEr  

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Bioconductor version: Release (3.17)

Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).

Author: Vanja Haberle [aut], Charles Plessy [cre], Damir Baranasic [ctb], Sarvesh Nikumbh [ctb]

Maintainer: Charles Plessy <charles.plessy at oist.jp>

Installation

To install this package, start R (version "4.3") 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")

 

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

Details

biocViews	Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version	2.6.1
In Bioconductor since	BioC 2.12 (R-3.0) (10.5 years)
License	GPL-3
Depends	methods, MultiAssayExperiment, R (>= 4.1.0)
Imports	BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table, DelayedArray, DelayedMatrixStats, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges(>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.18.0), KernSmooth, memoise, plyr, Rsamtools, reshape2, rtracklayer, S4Vectors(>= 0.27.5), som, stringdist, stringi, 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	seqArchRplus, seqPattern
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CAGEr_2.6.1.tar.gz
Windows Binary	CAGEr_2.6.1.zip
macOS Binary (x86_64)	CAGEr_2.6.1.tgz
macOS Binary (arm64)	CAGEr_2.6.1.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 3.17	Source Archive