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CAGEWorkflow

This is the development version of CAGEWorkflow; for the stable release version, see CAGEWorkflow.

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


Bioconductor version: Development (3.19)

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")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews AnnotationWorkflow, GeneExpressionWorkflow, Workflow
Version 1.19.0
License GPL-3
Depends R (>= 3.6.0), CAGEfightR, nanotubes
Imports
System Requirements
URL
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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
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Package Archives

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

Source Package CAGEWorkflow_1.19.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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/
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