To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("airway")
In most cases, you don't need to download the package archive at all.
airway
SummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
Bioconductor version: 3.0
This package provides a SummarizedExperiment 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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("airway")
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 |
| Reference Manual |
Details
| biocViews | ExperimentData, RNAseqData |
| Version | 1.0.0 |
| License | LGPL |
| Depends | R (>= 2.10), GenomicRanges |
| Imports | |
| LinkingTo | |
| Suggests | knitr, GEOquery |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | DESeq2 |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | airway_1.0.0.tar.gz |
| Windows Binary | airway_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | airway_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | airway_1.0.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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