CAGEfightR

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

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") and enter:

if (!require("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")

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

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version	1.20.0
In Bioconductor since	BioC 3.7 (R-3.5) (5.5 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)
Linking To
Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene
System Requirements
Enhances
URL	https://github.com/MalteThodberg/CAGEfightR
Bug Reports	https://github.com/MalteThodberg/CAGEfightR/issues

Depends On Me	CAGEWorkflow
Imports Me	CAGEr
Suggests Me	nanotubes
Links To Me
Build Report

Package Archives

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

Source Package	CAGEfightR_1.20.0.tar.gz
Windows Binary	CAGEfightR_1.20.0.zip
macOS Binary (x86_64)	CAGEfightR_1.20.0.tgz
macOS Binary (arm64)	CAGEfightR_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CAGEfightR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CAGEfightR
Bioc Package Browser	https://code.bioconductor.org/browse/CAGEfightR/
Package Short Url	https://bioconductor.org/packages/CAGEfightR/
Package Downloads Report	Download Stats