recipe bioconductor-etec16s

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment






16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin.

package bioconductor-etec16s

(downloads) docker_bioconductor-etec16s



depends bioconductor-biobase:


depends bioconductor-data-packages:


depends bioconductor-metagenomeseq:


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-etec16s

and update with::

   mamba update bioconductor-etec16s

To create a new environment, run:

mamba create --name myenvname bioconductor-etec16s

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-etec16s/tags`_ for valid values for ``<tag>``)

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