emtdata

DOI: 10.18129/B9.bioc.emtdata    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see emtdata.

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

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	emtdata
PDF		Reference Manual
Text		NEWS

Details

biocViews	ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData
Version	1.4.0
License	GPL-3
Depends	R (>= 4.1)
Imports	edgeR, ExperimentHub, SummarizedExperiment
LinkingTo
Suggests	testthat (>= 3.0.0), stringr, plyr, prettydoc, BiocStyle, Homo.sapiens, RColorBrewer, rmarkdown, BiocFileCache, knitr
SystemRequirements
Enhances
URL	https://github.com/DavisLaboratory/emtdata
BugReports	https://github.com/DavisLaboratory/emtdata/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	emtdata_1.4.0.tar.gz
Windows Binary
macOS Binary (x86_64)
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/
Package Downloads Report	Download Stats