Package: EMTscoreData 1.1.0

Haimei Wen

EMTscoreData: Single-cell RNA-seq datasets of EMT responses from Cook et al. (2020)

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.

Authors:Haimei Wen [aut, cre], Tian Hong [fnd]

EMTscoreData_1.1.0.tar.gz
EMTscoreData_1.1.0.tar.gz(r-4.7-any)EMTscoreData_1.1.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EMTscoreData/json (API)

# Install 'EMTscoreData' in R:

install.packages('EMTscoreData', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wenmm/emtscoredata/issues

On BioConductor:EMTscoreData-1.1.0(data/experiment 3.24)EMTscoreData-1.0.0(data/experiment 3.23)

experimenthub singlecelldata expressiondata cancerdata rnaseqdata datapkg

4.60 score 3 scripts 12 exports 174 dependencies

Last updated from:c9557df871. Checks:3 NOTE, 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
bioc-checks	NOTE	218
linux-devel	NOTE	1838
source / vignettes	OK	4892
linux-release	NOTE	3044

Exports:A549_EGF A549_TGFB1 A549_TNF DU145_EGF DU145_TGFB1 DU145_TNF MCF7_EGF MCF7_TGFB1 MCF7_TNF OVCA420_EGF OVCA420_TGFB1 OVCA420_TNF

Dependencies:abind AnnotationDbi AnnotationHub askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 bitops blob bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray deldir digest dotCall64 dplyr dqrng evaluate ExperimentHub farver fastDummies fastmap filelock fitdistrplus FNN fontawesome fs future future.apply generics GenomicRanges ggplot2 ggrepel ggridges globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr httr2 ica igraph IRanges irlba isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppThread RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra RSQLite Rtsne S4Arrays S4Vectors S7 sass scales scattermore sctransform Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable XVector yaml zoo

EMTscoreData Package

1. Introduction of EMTscoreData | 2. Installation | Install the development version from GitHub | Install from Bioconductor (recommended once available): | 3. Download data from the EMTscoreData R package | 3.1 Browse all EMTscoreData records | 3.2 Download data using the unique identifier: | 3.3 What is inside a SingleCellExperiment? | 4. Data analysis and visualization | 4.1 Load an EMT gene set (GMT) from Zenodo | 4.2 Calculating EMT Scores for Datasets Stored in EMTscoreData

Rendered fromEMTscoreData.Rmdusingknitr::rmarkdown

Last update: 2026-01-23
Started: 2025-12-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	A549_EGF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	A549_TGFB1
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	A549_TNF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	DU145_EGF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	DU145_TGFB1
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	DU145_TNF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	MCF7_EGF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	MCF7_TGFB1
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	MCF7_TNF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	OVCA420_EGF
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	OVCA420_TGFB1
EMTscoreData: Single-cell RNA-seq datasets for EMTscore	OVCA420_TNF