CAGEfightR

DOI: 10.18129/B9.bioc.CAGEfightR    

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

Bioconductor version: Release (3.7)

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 CAGE data analysis tasks. 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, calculation of TSS shapes and quantification of CAGE expression as expression matrices.

Author: Malte Thodberg

Maintainer: Malte Thodberg <maltethodberg at gmail.com>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("CAGEfightR")

Documentation

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 1.0.0
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, Matrix (>= 1.2-12), Matrix.utils (>= 0.9.6), grr, BiocGenerics(>= 0.24.0), S4Vectors(>= 0.16.0), IRanges(>= 2.12.0), GenomeInfoDb(>= 1.14.0), GenomicFeatures(>= 1.29.11), BiocParallel(>= 1.12.0), GenomicFiles(>= 1.14.0), Gviz(>= 1.22.2)
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
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package CAGEfightR_1.0.0.tar.gz
Windows Binary CAGEfightR_1.0.0.zip
Mac OS X 10.11 (El Capitan) CAGEfightR_1.0.0.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 http://bioconductor.org/packages/CAGEfightR/
Package Downloads Report Download Stats

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