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 (3.22)
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 "4.5") 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 | 1.25.0 |
| License | GPL-3 |
| Depends | R (>= 3.6.0), CAGEfightR, nanotubes |
| Imports | |
| System Requirements | |
| URL |
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 |
| Linking To | |
| Enhances | |
| 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_1.25.0.tar.gz |
| Windows Binary (x86_64) | |
| 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/ |
| Package Downloads Report | Download Stats |