recipe bioconductor-atena

Analysis of Transposable Elements






Quantify expression of transposable elements (TEs) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as output container of the quantified expression profiles. The implementation allows one to quantify TEs and gene transcripts in an integrated manner.

package bioconductor-atena

(downloads) docker_bioconductor-atena



depends bioconductor-annotationhub:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicalignments:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-rsamtools:


depends bioconductor-s4vectors:


depends bioconductor-sparsematrixstats:


depends bioconductor-summarizedexperiment:


depends r-base:


depends r-matrix:

depends r-matrixstats:

depends r-squarem:



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-atena

and update with::

   mamba update bioconductor-atena

To create a new environment, run:

mamba create --name myenvname bioconductor-atena

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-atena/tags`_ for valid values for ``<tag>``)

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