R packages integration with ArrayStudio

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Contents

General

OmicSoft has designed a convenient way to integrate lots of R packages for data analysis. Generally, user can setup the R Executable path in ArrayStudio, and all of the data analysis will be carried out in the R software.

R integration logic

  • User will have their own R software installed, and the according packages(library) installed in their R software
  • User can setup the R Executable path in ArrayStudio, so the data from ArrayStudio will be parsed into this R software for analysis
  • ArrayStudio will provide a GUI for users to conveniently select which data to analyze, and all the parameters for these packages will be provided as an option, default values will be assigned, but user can customize these paramters
  • When user click Run or Send to Server, the data and parameters will be parsed into R and get analyzed
  • When the analysis is done in R, ArrayStudio will take the output from R and import the result back into ArrayStudio (with some modifications in some cases)
  • User can easily view the table data and plot data with further customization in ArrayStudio

Warning.png WARNING: For all of the packages mentioned in this wiki, user will need to install the according library in their R software first


Supported packages

Currently, OmicSoft support the R packages as follows:

If user have other interested packages they would like to use with ArrayStudio, please contact with support@omicsoft.com and we will be happy to evaluate the feasibility.

R package configuration for local run

For local runs, version number can be found from the "Tools => R Integration => Setup R Script Engine" menu.

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If user don't see the box under column of Ready checked, user can check the box in the column of Install/Update, then click Update. This action will download the required rscript file from our server, keep the file in Scripts Directory (locally: OmicsoftHomeDirectory\RScripts by default), and then the box under Ready will be checked once the script is downloaded.

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R package integration for Server run

For server runs, version number can be found from the "Manage => Manage Scripts => Manage R Script Engine" menu (only admins can access this menu).

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If user don't see the box under column of Ready checked, user can check the box in the column of Install/Update, then click Update. This action will download the required rscript file from our server, keep the file in Scripts Directory (On server: BaseDirectory\Pipeline\RScripts by default), and then the box under Ready will be checked once the script is downloaded.

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