Analyses and Data Management
Analyses
In the Analyses tab, you'll see all the analyses in your study. The analyses will be displayed in card view by default. Each card will display the following information.
Analysis Name
Name of analysis.
Status
Status of analysis. See Analysis Statuses for a table of statuses and descriptions.
Analysis Type
Type of omic data used in the default or custom analysis.
Modified By
Last user who modified the analysis.
Date Modified
Date and time when the last update was made.
You can switch to list view by clicking the list icon in the top right. In the list view, you can customize the columns and filter your analyses.
Note that default analyses will be created automatically. This functionality will be applied to single cell RNA and spatial analyses.
Create Analysis
To create a new analysis, click 
.
Give your analysis a name and choose an analysis type from the dropdown menu.
Analysis Options
Default: Proteomic
General analysis pipeline for Illumina protein prep samples, with PCA and hierarchical clustering heatmap results
Default: Single Cell Transcriptomic
General analysis pipeline for Illumina single cell prep samples, including the processing steps to output PCA and UMAP visualizations
Default: Spatial Transcriptomics
General analysis pipeline for Illumina spatial prep samples, including a Spatial map with transcripts overlayed on the tissue image where each point is a grid. Graph-based clusters are also plotted on a UMAP and pie chart
Custom: 5-base Methylation
Starts with importing selected 5-base methylation data
Custom: Infinium Methylation
Starts with importing selected idat files
Custom: Proteomic
Starts with the quantified samples which have undergone prior normalization and offers flexible analysis options
Custom: RNA
Starts with salmon format sample counts that have not been normalized and offers flexible analyses options. The assembly and annotation model used in secondary analysis is required to annotate the features
Custom: Single Cell Transcriptomics
Starts with single cell counts and offers flexibility with the analyses pipeline step
Custom: Spatial Transcriptomics
Two starting nodes as cell-binned or grid-binned data, including the spatial image outputs, and offers flexibility with the analyses parameters
Custom: Third-party analysis
Starts with data import. This option appears only when third-party assay data has been uploaded.
Next, select the sample, sample group, or all samples for the analysis.
If all samples are chosen for the analysis, a sample group will be automatically added to the Sample Groups menu containing all of the samples in the analysis.
Run Analysis
Click 
to run the analysis. You will receive a notification that the analysis was successfully created.
Wait for the analysis status to change from "Pending" to "Complete".
Analysis Statuses
The following table describes the different analysis statuses.
Pending
The analysis has been initiated but has not yet started. It is waiting in the queue to be processed.
In Progress
The analysis is currently being executed. The system is processing the data and generating results.
Complete
The analysis has finished, and the results are ready to be viewed. Click into the analysis to view it.
Once the analysis is complete, you can click into it to view the results. Refer to the "Enter Analysis" section for more information on how to view your analysis.
Data Management
In the Data Management tab, you'll see a list of all the data and metadata files within your study. From here, you can delete files if needed.
Note that deleting data or metadata files will not remove any samples that were added to Connected Multiomics from those files. The samples will remain in Connected Multiomics even if the original files are deleted, ensuring that your sample data stays intact.
Last updated
Was this helpful?