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Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Bioconductor version: Release (3.19)

CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5'-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.

Author: Malte Thodberg

Maintainer: Malte Thodberg <maltethodberg at>

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


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:

Introduction to CAGEfightR HTML R Script
Reference Manual PDF


biocViews Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3 + file LICENSE
Depends R (>= 3.5), GenomicRanges(>= 1.30.1), rtracklayer(>= 1.38.2), SummarizedExperiment(>= 1.8.1)
Imports pryr (>= 0.1.3), assertthat (>= 0.2.0), methods (>= 3.6.3), Matrix (>= 1.2-12), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), GenomicAlignments(>= 1.22.1), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1)
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Suggests knitr, rmarkdown, BiocStyle,, TxDb.Mmusculus.UCSC.mm9.knownGene
Linking To
Depends On Me CAGEWorkflow
Imports Me CAGEr
Suggests Me nanotubes
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package CAGEfightR_1.24.0.tar.gz
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macOS Binary (x86_64) CAGEfightR_1.24.0.tgz
macOS Binary (arm64) CAGEfightR_1.24.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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