Download data from the emtdata R package | Accessing SummarizedExperiment object | Exploratory analysis and visualization | cursons2018 | cursons2015 | foroutan2017 | Session information
Package: emtdata 1.21.0
Malvika D. Kharbanda
emtdata: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)
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.
Authors:
emtdata_1.21.0.tar.gz
emtdata_1.21.0.tar.gz(r-4.7-any)emtdata_1.21.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
emtdata/json (API)
| # Install 'emtdata' in R: |
| install.packages('emtdata', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/davislaboratory/emtdata/issues
On BioConductor:emtdata-1.21.0(data/experiment 3.24)emtdata-1.20.0(data/experiment 3.23)
experimenthubhomo_sapiens_datarnaseqdataexpressiondatadatapkg
Last updated from:48bda00c06. Checks:1 ERROR, 2 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 | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 222 | ||
| linux-devel | NOTE | 331 | ||
| source / vignettes | OK | 321 | ||
| linux-release | NOTE | 349 |
Exports:asDGEListcursons2015_secursons2018_seforoutan2017_se
Dependencies:abindAnnotationDbiAnnotationHubaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrDelayedArraydplyredgeRExperimentHubfastmapfilelockgenericsGenomicRangesgluehttrhttr2IRangesjsonliteKEGGRESTlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngpurrrR6rappdirsrlangRSQLiteS4ArraysS4VectorsSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrswithrXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert a SummarizedExperiment object to a DGEList object | asDGEList |
| EGF or hypoxia treatment of Breast Cancer Cell lines from Cursons et al. (2015) | cursons2015_se |
| Combinatorial miRNAs in breast cancer EMT from Cursons et al. (2018) | cursons2018_se |
| TGFb stimulated cell lines from Foroutan et al. (2017) | foroutan2017_se |