CAGEfightR

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


Bioconductor version: Release (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")

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 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6.5 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)
System Requirements
URL https://github.com/MalteThodberg/CAGEfightR
Bug Reports https://github.com/MalteThodberg/CAGEfightR/issues
See More
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 CAGEfightR_1.24.0.tar.gz
Windows Binary (x86_64) CAGEfightR_1.24.0.zip (64-bit only)
macOS Binary (x86_64) CAGEfightR_1.24.0.tgz
macOS Binary (arm64) CAGEfightR_1.24.0.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