Module Score Workflow | Scribe

    Module Score Workflow

    • Jen Garbarino |
    • 11 steps |
    • 2 minutes
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    This workflow is used to look at the gene activity scores for multiple genes for a set of samples. It requires a create archrRProject output and a .csv file of genes of interest. Using archR's [[addModuleScore()]], this workflow outputs each sample and the UMAP distribution of the module. This is displayed in 2 ways, one where all the samples are on the same scale bar for easier comparison between samples and another where each sample is on its own scale bar to better visualize the variations within a sample.
    1
    Click on the workflows tab
    2
    Click module score to open the module score workflow
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    Select the size of the chip used for these samples
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    Next we select the create ArchRProject directory
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    Click "Select Folder" and navigate to the archRProject folder. For service generated projects this will be in Processed_Data. Otherwise this will be in the ArchRProjects folder.
    Click "Select Folder" and navigate to the archRProject folder. For service generated projects this will be in Processed_Data. Otherwise this will be in the ArchRProjects folder.
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    Enter the name for the project. This will be the name of the folder so incorporating the name of the gene list you are using is recommended
    7
    Next we will input the gene list we want to use for the module score
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    Click "Select File" and navigate to the .csv containing the list of genes you are interested in. This can be uploaded anywhere in the latchbio workspace.
    Click "Select File" and navigate to the .csv containing the list of genes you are interested in. This can be uploaded anywhere in the latchbio workspace.
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    Make sure your using the correct case for your species (uppercase for human, lowercase for mouse etc).
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    Next select where you want to save the output results of the workflow
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    Click "Select Folder" and navigate to where you would like to save the file
    Click "Select Folder" and navigate to where you would like to save the file
    11
    Click "Launch Workflow"