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airway

This is the development version of airway; for the stable release version, see airway.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("airway")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Airway smooth muscle cells HTML R Script
Reference Manual PDF

Details

biocViews ExperimentData, GEO, RNASeqData, SequencingData
Version 1.21.0
License LGPL
Depends R (>= 3.5.0), SummarizedExperiment
Imports
Linking To
Suggests knitr, GEOquery, markdown
System Requirements
Enhances
URL
See More
Depends On Me rnaseqGene
Imports Me consensusDE, NetActivity
Suggests Me apeglm, awst, biobroom, BioCor, BiocSet, CeTF, DelayedArray, DESeq2, EnhancedVolcano, EnrichmentBrowser, ExperimentSubset, ideal, IHW, IHWpaper, InteractiveComplexHeatmap, iSEEu, OPWeight, pathwayPCA, pcaExplorer, PCAtools, progeny, RegParallel, runibic, SummarizedExperiment, TTMap, weitrix
Links To Me
Build Report  

Package Archives

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

Source Package airway_1.21.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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 https://bioconductor.org/packages/airway/
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