recipe bioconductor-ffpe

Quality assessment and control for FFPE microarray expression data



GPL (>2)




biotools: ffpe

Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

package bioconductor-ffpe

(downloads) docker_bioconductor-ffpe



depends bioconductor-affy:


depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-lumi:


depends bioconductor-methylumi:


depends r-base:


depends r-sfsmisc:

depends r-ttr:



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-ffpe

and update with::

   mamba update bioconductor-ffpe

To create a new environment, run:

mamba create --name myenvname bioconductor-ffpe

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

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