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

Bioconductor version: Release (3.19)

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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews Clustering, FunctionalGenomics, GeneExpression, Normalization, Preprocessing, Sequencing, Software, Transcription, Visualization
Version 2.10.0
In Bioconductor since BioC 2.12 (R-3.0) (11.5 years)
License GPL-3
Depends methods, MultiAssayExperiment, R (>= 4.1.0)
Imports BiocGenerics, BiocParallel, BSgenome, CAGEfightR, data.table, DelayedArray, DelayedMatrixStats,, 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
System Requirements
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Suggests BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown
Linking To
Depends On Me
Imports Me
Suggests Me seqArchRplus, seqPattern
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package CAGEr_2.10.0.tar.gz
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macOS Binary (x86_64) CAGEr_2.10.0.tgz
macOS Binary (arm64) CAGEr_2.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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