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 decoded 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 | R script, Documentation |
| Update Sample Metadata | Update the Sample Metadata for a Study | R script, Documentation |
| Combine Sample Metadata | Generate Query Columns in Sample Metadata | Rscript, Documentation |
Export custom modules have an AtoMx v1.3.2 and v1.4.0 version. These modules are NOT interchangeable and must be run on their respective AtoMx versions. Each export module has an AtoMx_v1.3.2 folder that contains the older scripts.
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.