Package 'nanotubes'

Title: Mouse nanotube CAGE data
Description: Cap Analysis of Gene Expression (CAGE) data from "Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo" by Bornholdt et al. supplied as CAGE Transcription Start Sites (CTSSs).
Authors: Malte Thodberg
Maintainer: Malte Thodberg <[email protected]>
License: GPL-3
Version: 1.29.0
Built: 2026-10-10 10:40:55 UTC
Source: https://github.com/bioc/nanotubes

Help Index

CAGE data from mouse nanotube experiment

Description

Overview of the mouse nanotube CAGE experiment by Bornholdt et al. This experiment involved exposing mice to carbon nanotubes and performing Cap Analysis of Gene Expression (CAGE) on lung biopsies. The resulting CAGE Transcription Start Sites (CTSSs), the number of CAGE tag 5'-ends mapping to each genomic position, are supplied as BigWig-files (on mm9).

Usage

nanotubes

Format

Study design as a data.frame:

Class

Experimential group (factor): Ctrl (Untreated) or Nano (Treated with nanotubes)

Name

Name of sample

BigWigPlus

BigWig-file holding plus-strand CTSSs

BigWigPlus

BigWig-file holding plus-strand CTSSs

Source

https://pubs.acs.org/doi/10.1021/acsnano.6b07533

Examples

# BigWig import is only supported on non-windows platforms:
if (.Platform$OS.type != "windows") {
    library(GenomicRanges)
    library(rtracklayer)
    data(nanotubes)
    bw_path <- system.file("extdata",
                           nanotubes$BigWigMinus[1],
                           package="nanotubes",
                           mustWork = TRUE)
import(bw_path)
}