Obtaining sample information from GEO | Downloading FASTQ files from SRA | Aligning reads | Counting reads | Information on the RangedSummarizedExperiment | Information on the genes | Session information
Package: airway 1.33.2
Michael Love
airway: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014
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.
Authors:
airway_1.33.2.tar.gz
airway_1.33.2.tar.gz(r-4.7-any)airway_1.33.2.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
airway/json (API)
| # Install 'airway' in R: |
| install.packages('airway', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
On BioConductor:airway-1.33.2(data/experiment 3.24)airway-1.32.0(data/experiment 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
experimentdatasequencingdatarnaseqdatageodatapkg
Last updated from:54ec911b1c. Checks:1 ERROR, 2 WARNING, 1 OK. Indexed: yes.
This is a data package. Data packages may be large and do not get checked across all platforms.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 137 | ||
| linux-devel | WARNING | 206 | ||
| source / vignettes | OK | 262 | ||
| linux-release | WARNING | 252 |
Exports:
Dependencies:abindBiobaseBiocGenericsDelayedArraygenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsS4ArraysS4VectorsSeqinfoSparseArraySummarizedExperimentXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Airway smooth muscle cells | airway |
| Airway smooth muscle cells - Salmon quantification | gse |
