matdoering / openprimerui

**DEPRECATED** A Shiny Application for the openPrimeR R Package

The openPrimeR Shiny Application

Synopsis

openPrimeR is an R package providing methods for designing, evaluating,and comparing primer sets for multiplex polymerase chain reaction (PCR). The package provides a primer design function that generates novel primer setes by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. Moreover, existing primer sets can be evaluated according to their coverage and their fulfillment of constraints on the PCR-relevant physicochemical properties. For PCR tasks for which multiple possible primer sets exist, openPrimeR can facilitate the selection of the most suitable set by performing comparative analyses. The R package includes a Shiny application that provides a comprehensive and intuitive user interface for the core functionalites of the package.

More information

For more information on how to install openPrimeR, we refer to the corresponding user-space repository, which provides several installation routines.

Changelog

Take a look at the CHANGELOG to view recent changes to the project.

openprimerui's Issues

do not save results

Hi, dear

When I start openPrimerRui image in docker and start primer design - I have this page:

And when design ends, page is not updated and I'm not getting results(((

App Hangs on Startup

I'm having some issues getting the latest version App to load on startup. I have all of the suggested third-party tools installed on my Mac (R version 3.6.2) but can't figure out where it's getting stuck. I see the "Loading openPrimeR" message but it never successfully advances past this stage.

Any advice for things to look into would be much appreciated. Thanks!

sessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] shinyBS_0.61       shiny_1.4.0.2      openPrimeRui_1.8.0 openPrimeR_1.8.0  

loaded via a namespace (and not attached):
 [1] tidyselect_1.0.0        shinyjs_1.1             purrr_0.3.4             reshape2_1.4.4         
 [5] colorspace_1.4-1        vctrs_0.2.4             htmltools_0.4.0         stats4_3.6.2           
 [9] yaml_2.2.1              rlang_0.4.5             pillar_1.4.3            later_1.0.0            
[13] glue_1.4.0              BiocGenerics_0.32.0     RColorBrewer_1.1-2      GenomeInfoDbData_1.2.2 
[17] foreach_1.5.0           lifecycle_0.2.0         plyr_1.8.6              stringr_1.4.0          
[21] zlibbioc_1.32.0         Biostrings_2.54.0       munsell_0.5.0           gtable_0.3.0           
[25] htmlwidgets_1.5.1       lpSolveAPI_5.5.2.0-17.6 codetools_0.2-16        IRanges_2.20.2         
[29] fastmap_1.0.1           crosstalk_1.1.0.1       doParallel_1.0.15       httpuv_1.5.2           
[33] GenomeInfoDb_1.22.1     parallel_3.6.2          Rcpp_1.0.4.6            xtable_1.8-4           
[37] DT_0.13                 scales_1.1.0            promises_1.1.0          S4Vectors_0.24.4       
[41] jsonlite_1.6.1          XVector_0.26.0          mime_0.9                ggplot2_3.3.0          
[45] digest_0.6.25           stringi_1.4.6           dplyr_0.8.5             GenomicRanges_1.38.0   
[49] grid_3.6.2              tools_3.6.2             bitops_1.0-6            magrittr_1.5           
[53] RCurl_1.98-1.2          tibble_3.0.1            crayon_1.3.4            pkgconfig_2.0.3        
[57] ellipsis_0.3.0          assertthat_0.2.1        rstudioapi_0.11         iterators_1.0.12       
[61] R6_2.4.1                compiler_3.6.2