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

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.

Package details

AuthorMalte Thodberg
Bioconductor views Annotation Coverage DataImport DataRepresentation GeneExpression GeneRegulation GenomeBrowsers Normalization PeakDetection Preprocessing Sequencing Software Transcription Transcriptomics Visualization
MaintainerMalte Thodberg <[email protected]>
LicenseGPL-3 + file LICENSE
Version1.2.0
URL https://github.com/MalteThodberg/CAGEfightR
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEfightR")

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CAGEfightR documentation built on Nov. 1, 2018, 3:57 a.m.