CAGEWorkflow
This is the released version of CAGEWorkflow; for the devel version, see CAGEWorkflow.
A step-by-step guide to analyzing CAGE data using R/Bioconductor
Bioconductor version: Release (3.23)
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("CAGEWorkflow")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| CAGEWorkflow | HTML | R Script |
| NEWS | Text |
Details
| biocViews | AnnotationWorkflow, GeneExpressionWorkflow, Workflow |
| Version | 1.28.0 |
| 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |