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>

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

To install this package, start R (version "4.0") 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.

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

biocViews	AnnotationWorkflow, GeneExpressionWorkflow, Workflow
Version	1.4.0
License	GPL-3
Depends	R (>= 3.6.0), CAGEfightR, nanotubes
Imports
System Requirements
URL

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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me

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