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emtdata

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


Bioconductor version: Release (3.18)

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] , Chin Wee Tan [aut] , Dharmesh D. Bhuva [aut]

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 "4.3") and enter:


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

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

Details

biocViews ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData
Version 1.10.0
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
See More
Suggests testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
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Package Archives

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

Source Package emtdata_1.10.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/emtdata
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/emtdata
Package Short Url https://bioconductor.org/packages/emtdata/
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