DOI: 10.18129/B9.bioc.CAGEfightR    

This package is for version 3.7 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: 3.7

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 CAGE data analysis tasks. 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, calculation of TSS shapes and quantification of CAGE expression as expression matrices.

Author: Malte Thodberg

Maintainer: Malte Thodberg <maltethodberg at>

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biocViews Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version 1.0.0
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, 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)
Suggests knitr, rmarkdown, BiocStyle,, TxDb.Mmusculus.UCSC.mm9.knownGene
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