recipe bioconductor-emtdata

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

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/emtdata.html

License:

GPL-3

Recipe:

/bioconductor-emtdata/meta.yaml

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.

package bioconductor-emtdata

versions:

1.10.0-0,  1.8.0-0,  1.6.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-emtdata

and update with::

   mamba update bioconductor-emtdata

To create a new environment, run:

mamba create --name myenvname bioconductor-emtdata

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-emtdata:<tag>

(see `bioconductor-emtdata/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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