recipe bioconductor-rprimer

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/rprimer.html

License:

GPL-3

Recipe:

/bioconductor-rprimer/meta.yaml

Functions, workflow, and a Shiny application for visualizing sequence conservation and designing degenerate primers, probes, and (RT)-(q/d)PCR assays from a multiple DNA sequence alignment. The results can be presented in data frame format and visualized as dashboard-like plots. For more information, please see the package vignette.

package bioconductor-rprimer

versions:

1.6.0-0,  1.4.0-0,  1.2.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-bslib:

depends r-dt:

depends r-ggplot2:

depends r-mathjaxr:

depends r-patchwork:

depends r-reshape2:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinyfeedback:

requirements:

Installation

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-rprimer

and update with::

   mamba update bioconductor-rprimer

To create a new environment, run:

mamba create --name myenvname bioconductor-rprimer

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 quay.io/biocontainers/bioconductor-rprimer:<tag>

(see `bioconductor-rprimer/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rprimer/README.html)