emtdata

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

An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)

Bioconductor version: Development (3.21)

This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI.

Author: Malvika D. Kharbanda [aut, cre] (ORCID: ), Chin Wee Tan [aut] (ORCID: ), Dharmesh D. Bhuva [aut] (ORCID: )

Maintainer: Malvika D. Kharbanda <kharbanda.m at wehi.edu.au>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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

BiocManager::install("emtdata")

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("emtdata")

emtdata	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData
Version	1.15.0
License	GPL-3
Depends	R (>= 4.1)
Imports	edgeR, ExperimentHub, SummarizedExperiment
System Requirements
URL	https://github.com/DavisLaboratory/emtdata
Bug Reports	https://github.com/DavisLaboratory/emtdata/issues

Suggests	testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
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	emtdata_1.15.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/emtdata
Source Repository (Developer Access)	git clone [email protected]:packages/emtdata
Package Short Url	https://bioconductor.org/packages/emtdata/
Package Downloads Report	Download Stats