Analysis and Data Management
In the Analyses tab, you'll see all the analyses in your study. Multiple analyses can be performed on each study, user can use sample group to create a subset of the data to perform analysis, or choose different analysis type: default or custom to analyze the data in a study.
Card View vs List View
There are two types of display on Studies page and Analyses page. On the upper-right corner of the page, you can switch between the two view styles, card view vs list view.
In Card View, 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.
There are more controls in List view:
On column header, there is filter icon (
), it allows to filter the rows in the table based on the selected value:
Click on the 3 dots next to the filter icon (
) to sort the table, choose columns to display
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: Illumina Proteomics
General analysis pipeline for Illumina protein prep samples, with PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 9,000.
Default: Illumina Single Cell Transcriptomics
General analysis pipeline for Illumina single cell prep samples, including the processing steps to output PCA and UMAP plots, plus graph-based clustering visualizations.
For each sample, all features are reported and if feature ID's are not unique, Mean is used for Deduplication; raw counts are used as the count value format and cells with a total read count at least 400 are reported. The maximum samples for analysis is 1,000.
Default: Illumina Spatial Transcriptomics
General analysis pipeline for Illumina spatial 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. The maximum samples for analysis is 100.
Default: Illumina Bulk Transcriptomics
General analysis pipeline for Illumina mRNA and Total RNA prep samples including PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 500.
Default: Illumina miRNA
General analysis pipeline for Illumina miRNA prep samples including PCA and hierarchical clustering heatmap results. The maximum samples for analysis is 500.
Default: Illumina 5-base DNA Methylation
General analysis pipeline for 5-base DNA prep samples including regional methylation PCA plots, k-means clustering, and QC. The maximum samples for analysis is 200.
Custom: Multiomics
Available inputs include Illumina proteomics, single cell, spatial, and bulk transcriptomics, miRNA, 5-base DNA and Infinium methylation as well as third-party data types including Seurat (RNA), Seurat (ATAC), Somalogic ADAT, Gene counts in sf Format, and VCF. Two or more data types can be analyzed together in any combination.
Custom: Illumina Proteomics
Starts with the quantified samples which have undergone prior normalization and offers flexible analysis options. The maximum samples for analysis is 9,000.
Custom: Illumina Single Cell Transcriptomics
Starts with single cell counts and offers flexibility with the analyses pipeline step. For each sample, all features are reported and if feature ID's are not unique, Mean is used for Deduplication; raw counts are used as the count value format and cells with a total read count at least 400 are reported. The maximum samples for analysis is 1,000.
Custom: Illumina Spatial Transcriptomics
Two starting nodes as cell-binned or grid-binned data, including the spatial image outputs, and offers flexibility with the analyses parameters. The maximum samples for analysis is 100.
Custom: Illumina Bulk Transcriptomics
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. The maximum samples for analysis is 500.
Custom: Illumina miRNA
Starts with imported count matrix that have not been normalized and offers flexible analysis options. The maximum samples for analysis is 500.
Custom: Illumina 5-base DNA Methylation
Starts with importing selected 5-base methylation data and offers flexible analysis options. The maximum samples for analysis is 200.
Custom: Illumina Infinium Methylation
Starts with importing selected idat files and offers flexible analysis options.
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.
Current spatial multisample analysis does not yet support the import of a mix of samples that use pipeline-manifest.json and samples that do not. When running an analysis on a sample group that has both types of samples, only those samples with a pipeline-manifest.json file will import.
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.
Error
The analysis has ended in error. Using the Analysis tab list view, click the info icon 
to get more information about the error type. The error can be further diagnosed using the Inspect analysis link.
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
In the Data tab, you'll see a list of all the data and metadata files within your study from which your samples are derived.
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.
Study Settings
On the study page, there is a setting gear button allow more advanced editing for study.
Study name, description and preferred project can be edited.
When select Automatically create single sample default analyses, scRNA-seq and Spatial transcriptomic assay will automatically perform analysis on each sample separately.
When select Automatically import data from pipelines, new generated samples in preferred ICA project in the selected assay will be automatically created.
Click Update to save the change.
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