CAGEfightR

This is the development version of CAGEfightR; for the stable release version, see CAGEfightR.

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

Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("CAGEfightR")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, Coverage, DataImport, DataRepresentation, GeneExpression, GeneRegulation, GenomeBrowsers, Normalization, PeakDetection, Preprocessing, Sequencing, Software, Transcription, Transcriptomics, Visualization
Version	1.23.0
In Bioconductor since	BioC 3.7 (R-3.5) (6 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)
System Requirements
URL	https://github.com/MalteThodberg/CAGEfightR
Bug Reports	https://github.com/MalteThodberg/CAGEfightR/issues

Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene
Linking To
Enhances
Depends On Me	CAGEWorkflow
Imports Me	CAGEr
Suggests Me	nanotubes
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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