EMTscoreData
This is the released version of EMTscoreData; for the devel version, see EMTscoreData.
Single-cell RNA-seq datasets of EMT responses from Cook et al. (2020)
Bioconductor version: Release (3.23)
Provides 12 single-cell RNA-seq datasets profiling epithelial–mesenchymal transition (EMT) in human cancer cell lines (MCF7, OVCA420, DU145, and A549) under TGF-beta stimulation, kinase inhibition, and time-course conditions, as reported by Cook DP and Vanderhyden BC (2020). The datasets are distributed via ExperimentHub as SingleCellExperiment objects.
Author: Haimei Wen [aut, cre]
, Tian Hong [fnd]
Maintainer: Haimei Wen <hudie.luoluo at gmail.com>
citation("EMTscoreData")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("EMTscoreData")
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("EMTscoreData")| EMTscoreData Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | CancerData, ExperimentData, ExperimentHub, ExpressionData, RNASeqData, SingleCellData |
| Version | 1.0.0 |
| License | GPL-3 |
| Depends | |
| Imports | SummarizedExperiment, Seurat, SingleCellExperiment, AnnotationHub, ExperimentHub, ggplot2 |
| System Requirements | |
| URL | https://github.com/wenmm/EMTscoreData |
| Bug Reports | https://github.com/wenmm/EMTscoreData/issues |
See More
| Suggests | BiocFileCache, SeuratObject, knitr, rmarkdown, googledrive, BiocStyle, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EMTscoreData_1.0.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/EMTscoreData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EMTscoreData |
| Package Short Url | https://bioconductor.org/packages/EMTscoreData/ |
| Package Downloads Report | Download Stats |