CAGEWorkflow

DOI: 10.18129/B9.bioc.CAGEWorkflow    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see CAGEWorkflow.

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

Bioconductor version: 3.11

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	CAGEWorkflow
Text		NEWS

Details

biocViews	AnnotationWorkflow, GeneExpressionWorkflow, Workflow
Version	1.4.0
License	GPL-3
Depends	R (>= 3.6.0), CAGEfightR, nanotubes
Imports
LinkingTo
Suggests	knitr, kableExtra, 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
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	CAGEWorkflow_1.4.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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