- recipe bioconductor-openprimer
Multiplex PCR Primer Design and Analysis
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/openPrimeR.html
- License:
GPL-2
- Recipe:
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:
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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-openprimer/README.html)