CAGEfightR

DOI: 10.18129/B9.bioc.CAGEfightR    

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

Bioconductor version: Release (3.13)

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 gmail.com>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CAGEfightR")

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

Documentation

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

browseVignettes("CAGEfightR")

 

HTML	R Script	Introduction to CAGEfightR
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 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)
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene
SystemRequirements
Enhances
URL	https://github.com/MalteThodberg/CAGEfightR
BugReports	https://github.com/MalteThodberg/CAGEfightR/issues
Depends On Me	CAGEWorkflow
Imports Me
Suggests Me	nanotubes
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	CAGEfightR_1.12.0.tar.gz
Windows Binary	CAGEfightR_1.12.0.zip
macOS 10.13 (High Sierra)	CAGEfightR_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CAGEfightR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CAGEfightR
Package Short Url	https://bioconductor.org/packages/CAGEfightR/
Package Downloads Report	Download Stats