airway

DOI: 10.18129/B9.bioc.airway    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see airway.

RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014

Bioconductor version: 3.8

This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. 'RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

Author: Michael Love

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

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

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("airway")

 

HTML	R Script	Airway smooth muscle cells
PDF		Reference Manual

Details

biocViews	ExperimentData, GEO, RNASeqData, SequencingData
Version	1.2.0
License	LGPL
Depends	R (>= 2.10), SummarizedExperiment
Imports
LinkingTo
Suggests	knitr, GEOquery
SystemRequirements
Enhances
URL
Depends On Me	rnaseqGene
Imports Me	consensusDE
Suggests Me	adaptest, apeglm, biobroom, BioCor, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ideal, IHW, IHWpaper, OPWeight, pcaExplorer, progeny, RegParallel, runibic, SummarizedExperiment, ToPASeq, TTMap
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	airway_1.2.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/airway
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/airway
Package Short Url	http://bioconductor.org/packages/airway/
Package Downloads Report	Download Stats