recipe bioconductor-bgeecall

Automatic RNA-Seq present/absent gene expression calls generation



GPL-3 + file LICENSE



BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (

package bioconductor-bgeecall

(downloads) docker_bioconductor-bgeecall



depends bioconductor-biomart:


depends bioconductor-biostrings:


depends bioconductor-genomicfeatures:


depends bioconductor-rhdf5:


depends bioconductor-rtracklayer:


depends bioconductor-tximport:


depends r-base:


depends r-data.table:

depends r-dplyr:

depends r-jsonlite:

depends r-rslurm:

depends r-sjmisc:



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-bgeecall

and update with::

   mamba update bioconductor-bgeecall

To create a new environment, run:

mamba create --name myenvname bioconductor-bgeecall

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

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