Neighborhood Analysis Workflow | Scribe

    Neighborhood Analysis Workflow

    • Jen Garbarino |
    • 20 steps |
    • 2 minutes
    information ordinal icon
    Neighborhood analysis calculates how often each cluster is spatially adajcent to another cluster for a set of samples. This analysis is based on the paper linked here:[https://www.cell.com/cell-metabolism/fulltext/S1550-4131(21)00363-6?\\\_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1550413121003636%3Fshowall%3Dtrue](https://www.cell.com/cell-metabolism/fulltext/S1550-4131\(21\)00363-6?%5C_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1550413121003636%3Fshowall%3Dtrue)
    alert ordinal icon
    Alert! Workflow is not compatible with 2 or more FG220 runs. These samples need to be run individually through the workflow.
    1
    Click on the workflows icon to go to the workflow tab
    2
    Click on neighborhood analysis workflow
    3
    Click Add Row to add the first sample
    4
    Enter the Run_id here. Run_id MUST be the name of the Seurat object
    alert ordinal icon
    Workflow will fail if Run_id does not match Seraut object name
    5
    Here we input the Seurat Object which contains the spatial location for each data point
    6
    Click "Select File" and navigate to the Seurat Object for this sample. This will be in Processed_Data or in the ArchRProjects folder if generated from the create archRProject workflow in this workspace. Press select when
    Click "Select File" and navigate to the Seurat Object for this sample. This will be in Processed_Data or in the ArchRProjects folder if generated from the create archRProject workflow in this workspace. Press select when
    alert ordinal icon
    Make sure to use the SeuratObj.rds file not the SeuratObjMotif.rds file
    7
    Enter Condition if applicable
    8
    Next we input the spatial folder location in the Spatial_dir field
    9
    Click "Select Folder" and navigate to the spatial folder for this sample. This will be located in Raw_data for service runs or was generated by AtlasXBrowser in this workspace in the spatials folder
    Click "Select Folder" and navigate to the spatial folder for this sample. This will be located in Raw_data for service runs or was generated by AtlasXBrowser in this workspace in the spatials folder
    10
    Next we input the tissue_position_list.csv location in the positions_file field
    11
    Click "Select Folder" and navigate to the tissue_positions_list.csv for this sample. Click select
    Click "Select Folder" and navigate to the tissue_positions_list.csv for this sample. Click select
    12
    Add Row for every sample used in the comparison
    13
    Select the genome for your samples in the genome field
    14
    Give the project a name. This will be the name of the folder the data is saved
    15
    Click "Launch Workflow"
    16
    Once workflow is finished navigate to <https://console.latch.bio/data>