CAGEWorkflow

DOI: 10.18129/B9.bioc.CAGEWorkflow    

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

Bioconductor version: Release (3.9)

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 "3.6") 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")

 

PDF R Script CAGEWorkflow

Details

biocViews AnnotationWorkflow, GeneExpressionWorkflow, Workflow
Version 1.0.0
License GPL-3
Depends R (>= 3.6.0), nanotubes
Imports
LinkingTo
Suggests knitr, rmarkdown, BiocWorkflowTools, pheatmap, ggseqlogo, viridis, magrittr, ggforce, ggthemes, tidyverse, dplyr, CAGEfightR, 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_1.0.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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

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