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("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 | ||
| 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 |