recipe bioconductor-single.mtec.transcriptomes

Single Cell Transcriptome Data and Analysis of Mouse mTEC cells






This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.

package bioconductor-single.mtec.transcriptomes

(downloads) docker_bioconductor-single.mtec.transcriptomes



depends bioconductor-data-packages:


depends curl:

depends r-base:




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-single.mtec.transcriptomes

and update with::

   mamba update bioconductor-single.mtec.transcriptomes

To create a new environment, run:

mamba create --name myenvname bioconductor-single.mtec.transcriptomes

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<tag>

(see `bioconductor-single.mtec.transcriptomes/tags`_ for valid values for ``<tag>``)

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