phanstiellab / coralp Goto Github PK

Part of JOSS review (openjournals/joss-reviews#1837):

Could you add installation instructions? There is a list of R packages dependencies but no information about the installation of CoralP itself. Would be good as well to convert it to an R package [1-2].

[1] https://cran.r-project.org/doc/manuals/r-release/R-exts.html
[2] http://r-pkgs.had.co.nz/

Part of JOSS review (openjournals/joss-reviews#1837):

Could you fix the legend of figure 1? i.e.: "Figure 1: Figure1. ....", there is a duplication of "Figure 1".

There is also a problem with the reference Bailey2015-ft which is not considered during the generation of the pdf.

I am trying to run the shiny app from my mac locally.
when I type the command I get the following. Can you tell me why I am getting this error?
Thank you.

> shiny::runApp()
Loading required package: shiny

Attaching package: ‘shinydashboard’

The following object is masked from ‘package:graphics’:

    box

Linking to librsvg 2.48.4

Attaching package: ‘colourpicker’

The following object is masked from ‘package:shiny’:

    runExample

Attaching package: ‘DT’

The following objects are masked from ‘package:shiny’:

    dataTableOutput, renderDataTable

Attaching package: ‘jsonlite’

The following object is masked from ‘package:shiny’:

    validate

Error in dots_list(...) : object 'outputjsonshort' not found    

Hello,
I am a Postdoctoral researcher working in Angus Nairn’s lab, Department of Psychiatry, Yale University. We used a proximity labelling proteomics approach to identify the protein interactome of a brain phosphoprotein in rats. We identified 1945 proximal proteins (organism: rat) to this phosphoprotein. We used CORALP software to identify the phosphatases and kinases in the proximal protein interactome.
Though the software identified and plotted PPIs with hierarchical information, there are lots of isoforms which are missing. For example, the software identified PPP2CB but not PPP2R2A, PPP2R5D, PPP1R9A. Like this many phosphatases were not identified. We believe that the proteins which were not identified are not in the phosphatase database of the software. The same happened with kinases as well.
We would like to know if there is an updated version of the software that could include these missing phosphatases and kinase isoforms? We would appreciate it if you could suggest some solutions.
Thank you for your time.
Boby

When I type in a string in the search box I get the following error message window popup. It also shows the same message when I click the sort arrow in the column.

DataTables warning: table id=DataTables_Table_17 - Error in tolower(x): invalid input 'Protein Phosphatase 1 Catalytic Subunit Beta<ca>' in 'utf8towcs'