DOI: 10.18129/B9.bioc.CAGEfightR    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CAGEfightR.

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

Bioconductor version: 3.10

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")):


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biocViews Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version 1.6.0
In Bioconductor since BioC 3.7 (R-3.5) (2 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, Matrix (>= 1.2-12), Matrix.utils (>= 0.9.6), grr (>= 0.9.5), BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2), InteractionSet(>= 1.9.4), GenomicInteractions(>= 1.15.1)
Suggests knitr, rmarkdown, BiocStyle,, TxDb.Mmusculus.UCSC.mm9.knownGene
Depends On Me CAGEWorkflow
Imports Me
Suggests Me nanotubes
Links To Me
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