Registration Open for Bioc2024
Early registration discount pricing ends May 31!

CAGEr

This is the development version of CAGEr; for the stable 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: Development (3.20)

The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.

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

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

Citation (from within R, enter citation("CAGEr")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 2.11.3
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-3
Depends methods, MultiAssayExperiment, R (>= 4.1.0)
Imports BiocGenerics, BiocParallel, Biostrings, BSgenome, CAGEfightR, data.table, formula.tools, GenomeInfoDb, GenomicAlignments, GenomicRanges(>= 1.37.16), ggplot2 (>= 2.2.0), gtools, IRanges(>= 2.18.0), KernSmooth, memoise, plyr, rlang, Rsamtools, reshape2, rtracklayer, S4Vectors(>= 0.27.5), scales, som, stringdist, stringi, SummarizedExperiment, utils, vegan, VGAM
System Requirements
URL
See More
Suggests BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Drerio.UCSC.danRer7, BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9, DESeq2, FANTOM3and4CAGE, ggseqlogo, BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me seqArchRplus, seqPattern
Links To Me
Build Report Build Report

Package Archives

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

Source Package CAGEr_2.11.3.tar.gz
Windows Binary CAGEr_2.11.2.zip
macOS Binary (x86_64) CAGEr_2.11.3.tgz
macOS Binary (arm64) CAGEr_2.11.2.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