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>

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

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

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