recipe bioconductor-openprimer

Multiplex PCR Primer Design and Analysis

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/openPrimeR.html

License:

GPL-2

Recipe:

/bioconductor-openprimer/meta.yaml

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

Versions:

1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.1-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.1-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-decipher >=2.26.0,<2.27.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• mafft >=7.305

• r-ape >=3.5

• r-base >=4.2,<4.3.0a0

• r-digest >=0.6.9

• r-distr >=2.6

• r-distrex >=2.6

• r-dplyr >=0.5.0

• r-fitdistrplus >=1.0-7

• r-foreach >=1.4.3

• r-ggplot2 >=2.1.0

• r-hmisc >=3.17-4

• r-lpsolveapi >=5.5.2.0-17

• r-magrittr >=1.5

• r-openxlsx >=4.0.17

• r-plyr >=1.8.4

• r-rcolorbrewer >=1.1-2

• r-reshape2 >=1.4.1

• r-scales >=0.4.0

• r-seqinr >=3.3-3

• r-stringdist >=0.9.4.1

• r-stringr >=1.0.0

• r-uniqtag >=1.0

• r-xml >=3.98-1.4

Required By:

• bioconductor-openprimerui

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-openprimer

and update with:

conda update bioconductor-openprimer

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-openprimer:<tag>

(see bioconductor-openprimer/tags for valid values for <tag>)

Download stats

Link to this page

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