This repository contains R script that can be used in custom modules in the AtoMx SMIDA.
| Name | Description | Links |
|---|---|---|
| Export | Export all files associated with current study: Seurat, TileDB array, and/or raw files. | R script, Documentation |
| Flat File Export | Export Flat files used in Seurat's LoadNanostring function | R script, Documentation |
| RNA QC Plots | Summary plots of CosMx SMI RNA QC | R script, Documentation |
| Get Sample Metadata | Get the Sample Metadata for a Study (Non-China Release*) | R script, Documentation |
| Update Sample Metadata | Update the Sample Metadata for a Study (Non-China Release*) | R script, Documentation |
* Non-China releases have not been verified in an AtoMx China tenant. Once verified on a China tenant this disclaimer will be removed.
Download R script from NanoString website or GitHub
Instructions from User Manual
From the Pipeline Run panel, click the custom modules icon.
The Custom Modules window opens. Edit or delete existing custom modules with the pencil and trash icons, respectively.
To add a new custom module to the pipeline, click Add Module. The Add New Module window opens. Enter information about the new module, including name (required), description, parameters, packages (click + to input package information), arguments (click + to input arguments), and/or entry point. Additionally, you can upload custom script files. Variables required and recommended parameters for individual scripts will be located in the CosMxDA[ModuleName]Setup.docx file in each folder.
Click Save to exit and add the defined module to the Custom Modules list, or exit without saving by clicking the x in the top right.