recipe bioconductor-openprimer

Multiplex PCR Primer Design and Analysis






An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the 'openPrimeRui' package.

package bioconductor-openprimer

(downloads) docker_bioconductor-openprimer



depends bioconductor-biocgenerics:


depends bioconductor-biostrings:


depends bioconductor-decipher:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-s4vectors:


depends mafft:


depends r-ape:


depends r-base:


depends r-digest:


depends r-distr:


depends r-distrex:


depends r-dplyr:


depends r-fitdistrplus:


depends r-foreach:


depends r-ggplot2:


depends r-hmisc:


depends r-lpsolveapi:


depends r-magrittr:


depends r-openxlsx:


depends r-plyr:


depends r-rcolorbrewer:


depends r-reshape2:


depends r-scales:


depends r-seqinr:


depends r-stringdist:


depends r-stringr:


depends r-uniqtag:


depends r-xml:




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-openprimer

and update with::

   mamba update bioconductor-openprimer

To create a new environment, run:

mamba create --name myenvname bioconductor-openprimer

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

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