In MalteThodberg/nanotubes: Mouse nanotube CAGE data

Installation

Install the most recent stable version from Bioconductor:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("nanotubes")

And load nanotubes:

library(nanotubes)

Alternatively, you can install the development version directly from GitHub using devtools:

devtools::install_github("MalteThodberg/nanotubes")

Citation

If you use nanotubes, please cite the following article:

citation("nanotubes")

Getting help

For general questions about the usage of nanotubes, use the official Bioconductor support forum and tag your question "nanotubes". We strive to answer questions as quickly as possible.

For technical questions, bug reports and suggestions for new features, we refer to the nanotubes github page

Data description

CAGE Transcription Start Sites (CTSSs), the number of CAGE tag 5'-end mapping to each genomic location data was obtained from the authors of the original study. Remaining data used in the study can be downloaded from GSE70386.

One technical replicate was not included.

Accessing study design and BigWig-Files

Load the data into R to get an overview of the included samples:

data("nanotubes")
knitr::kable(nanotubes)

Load a data from a BigWig-file into R using the r BiocStyle::Biocpkg("rtracklayer") package:

library(rtracklayer)
bw_fname <- system.file("extdata", nanotubes$BigWigPlus[1], 
                        package = "nanotubes", 
                        mustWork = TRUE)
import(bw_fname)

Importing into CAGEfightR

The data contained in the package is correctly formatted for analysis with the r BiocStyle::Biocpkg("CAGEfightR") package:

library(CAGEfightR)

# Setup paths
bw_plus <- system.file("extdata", nanotubes$BigWigPlus, 
                        package = "nanotubes", 
                        mustWork = TRUE)
bw_minus <- system.file("extdata", nanotubes$BigWigMinus, 
                        package = "nanotubes", 
                        mustWork = TRUE)

# Save as named BigWigFileList
bw_plus <- BigWigFileList(bw_plus)
bw_minus <- BigWigFileList(bw_minus)
names(bw_plus) <- names(bw_minus) <- nanotubes$Name

# Quantify
CTSSs <- quantifyCTSSs(bw_plus, bw_minus, design=nanotubes)