CAGEWorkflow

This is the released version of CAGEWorkflow; for the devel version, see CAGEWorkflow.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9

A step-by-step guide to analyzing CAGE data using R/Bioconductor

Bioconductor version: Release (3.23)

Workflow for analyzing Cap Analysis of Gene Expression (CAGE) data using R/Bioconductor.

Author: Malte Thodberg [aut, cre]

Maintainer: Malte Thodberg <maltethodberg at gmail.com>

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

Malte Thodberg. CAGEWorkflow: A step-by-step guide to analyzing CAGE data using R/Bioconductor. doi:10.18129/B9.bioc.CAGEWorkflow, R package version 1.28.0, https://bioconductor.org/packages/CAGEWorkflow.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

BiocManager::install("CAGEWorkflow")

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("CAGEWorkflow")

CAGEWorkflow	HTML	R Script
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationWorkflow, GeneExpressionWorkflow, Workflow
Version	1.28.0
In Bioconductor since	BioC 3.9 (R-3.6) (7.5 years)
License	GPL-3
Depends	R (>= 3.6.0), CAGEfightR, nanotubes
Imports
System Requirements
URL

Suggests	knitr, magick, rmarkdown, BiocStyle, BiocWorkflowTools, pheatmap, ggseqlogo, viridis, magrittr, ggforce, ggthemes, tidyverse, dplyr, GenomicRanges, SummarizedExperiment, GenomicFeatures, BiocParallel, InteractionSet, Gviz, DESeq2, limma, edgeR, statmod, BiasedUrn, sva, TFBSTools, motifmatchr, pathview, BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, JASPAR2016, png
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	CAGEWorkflow_1.28.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CAGEWorkflow
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CAGEWorkflow
Package Short Url	https://bioconductor.org/packages/CAGEWorkflow/
Package Downloads Report	Download Stats