CAGEWorkflow

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see CAGEWorkflow.

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

Installation

To install this package, start R (version "4.5") 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")

Details

See More

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