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• Introduction
  • The concept of CLC Single Cell Analysis Module
  • Contact information
  • System requirements
  • Installing modules
    • Licensing modules
    • Uninstalling modules
  • Installing server extensions
    • Licensing server extensions
• Reference data management
  • QIAGEN Sets
• Running tools and workflows
• Data import
  • Import Cell Annotations
  • Import Cell Clusters
  • Import Cell Clonotypes
  • Import Expression Matrix
    • HDF5 formats
    • Other formats
  • Import Peak Count Matrix
  • Import Space Ranger
  • Cell format in importers
  • Import Immune Reference Segments
    • IMSEQ
    • IMGT
    • Output from Import Immune Reference Segments
• Data export
  • Export Cell Ranger HDF5 Expression Matrix
  • Export AnnData Expression Matrix
  • Export h5Seurat Expression Matrix
  • Export Loom Expression Matrix
  • Export MEX Expression Matrix
  • Export Plain Text Table Expression Matrix
  • Export Peak Count Matrix
• Prepare Reads
  • Annotate Single Cell Reads
    • Read structure
    • Barcodes from names
    • Barcode correction
    • Sample name
    • The output of Annotate Single Cell Reads
• Creating a Gene Expression Matrix
  • Single Cell RNA-Seq Analysis
    • The Single Cell RNA-Seq Analysis report
    • The Single Cell RNA-Seq Analysis algorithm
  • QC for Single Cell
    • Empty droplets filter
    • Count-based and extra-chromosomal filters
    • Doublets filter
    • The output of QC for Single Cell
    • Choosing barcodes to retain
    • Cell calling
    • Automatic thresholds
    • Doublet calling
  • Demultiplex Parse Bio Samples
  • Normalize Single Cell Data
    • When is batch correction appropriate?
    • The output of Normalize Single Cell Data
    • The Normalize Single Cell Data algorithm
  • The Expression Matrix element
• Cell Type Classification
  • Browse QIAGEN Cell Ontology
  • Predict Cell Types
    • The output of Predict Cell Types
    • Cell type refinement
  • Train Cell Type Classifier
    • Features used for training and prediction
    • The output of Train Cell Type Classifier
    • SVMs for cell type classification
  • Update Cell Type Classifier
  • The Cell Type Classifier element
• Expression Analysis
  • Differential Expression for Single Cell
    • The output of Differential Expression for Single Cell
    • The differential expression algorithm
  • Create Expression Plot
    • The Heat Map output of Create Expression Plot
    • The Dot Plot output of Create Expression Plot
    • The Violin Plot output of Create Expression Plot
• Velocity Analysis
  • Single Cell Velocity Analysis
    • The output of Single Cell Velocity Analysis
    • The velocity estimation algorithm
  • Differential Velocity for Single Cell
  • Score Velocity Genes
    • The output of Score Velocity Genes
  • Create Phase Portrait Plot
  • Velocity analysis in workflows
  • The Velocity Matrix element
• Spatial Transcriptomics
  • The Spatial Transcriptomics Plot element
• Chromatin Accessibility
  • Single Cell ATAC-Seq Analysis
    • The output of Single Cell ATAC-Seq Analysis
    • The report output from Single Cell ATAC-Seq Analysis
    • The Single Cell ATAC-Seq Analysis algorithm
  • Split Read Mapping by Cell
  • Differential Accessibility for Single Cell
    • The differential accessibility algorithm
  • The Peak Count Matrix element
• Immune Repertoire
  • Single Cell V(D)J-Seq Analysis
    • The report output from Single Cell V(D)J-Seq Analysis
    • The clonotype identification algorithm
  • Filter Cell Clonotypes
  • Combine Cell Clonotypes
  • Compare Cell Clonotypes
    • The output of Compare Cell Clonotypes
  • Convert Clonotypes to Cell Annotations
  • The Cell Clonotypes element
    • Primary and secondary clonotypes
    • Cell Clonotypes tables
    • Cell Clonotypes alignments
    • Cell Clonotypes Sankey plot
• Noise reduction through feature selection and dimensionality reduction
  • Feature selection and dimensionality reduction
    • Calculation of estimated biological variation
• Cell Annotation
  • Cluster Single Cell Data
    • The Cluster Single Cell Data algorithm
  • Create Heat Map for Cell Abundance
    • The output of Create Heat Map for Cell Abundance
  • Create Cell Annotations from Hashtags
  • The Cell Annotations element
  • The Cell Clusters element
• Dimensionality reduction
  • UMAP for Single Cell
  • tSNE for Single Cell
• Single cell low-dimensional plots functionality
  • Manual annotation
  • Visualizing different types of matrices
  • Create Subset
  • Extract to Table
  • Launching of Create Expression Plot
  • Launching of Create Heat Map for Cell Abundance
  • Launching of Differential Accessibility for Single Cell
  • Launching of Differential Expression for Single Cell
  • Launching of Differential Velocity for Single Cell
  • Launching of Score Velocity Genes
• Utility tools
  • Combine Cell Annotations
  • Update Cell Annotations
  • Convert Metadata to Cell Annotations
  • Combine Cell Clusters
  • Update Cell Clusters
  • Add Information to Plot
  • Update Single Cell Sample Name
• Single cell template workflows from reads
  • Expression Analysis from Reads
    • Configuring the batch units for Expression Analysis from Reads
    • Output from Expression Analysis from Reads
  • Chromatin Accessibility Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility Analysis from Reads
    • Output from Chromatin Accessibility Analysis from Reads
  • Chromatin Accessibility and Expression Analysis from Reads
    • Configuring the batch units for Chromatin Accessibility and Expression Analysis from Reads
    • Output from Chromatin Accessibility and Expression Analysis from Reads
    • Importing reads
  • Immune Repertoire Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire Analysis from Reads (10xV(D)J)
  • Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Configuring the batch units for Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
    • Output from Immune Repertoire and Expression Analysis from Reads (10xV(D)J)
• Single cell template workflows from imported data
  • Expression Analysis from Matrix
    • Output from Expression Analysis from Matrix
  • Chromatin Accessibility and Expression Analysis from Matrix
    • Output of Chromatin Accessibility and Expression Analysis from Matrix
  • Immune Repertoire and Expression Analysis from Clonotypes and Matrix
    • Output from Immune Repertoire and Expression Analysis from Clonotypes and Matrix
  • Importing data
• Bibliography

Expression Analysis from Matrix

The workflow Expression Analysis from Matrix takes one or more Expression Matrix () / () as input and performs quality control, normalization, clustering, and cell type prediction. If enabled during execution, velocity analysis is also performed. The workflow uses iterate functionality and allows for a combined analysis of multiple samples to produce:

• a single, multi-sample, normalized Expression Matrix () / ();
• a Dimensionality Reduction Plot () associated with the automated clusters, predicted cell types and additional cell annotations;
• a Heat Map (), a Dot Plot (), and a Violin Plot () with the predicted cell types as cell groups;
• a Cell Abundance Heat Map () with the automated clusters and predicted cell types as cell groups.
• If velocity analysis is enabled during execution:
  • a Phase Portrait Plot () with per gene information on the velocity dynamics;
  • a Velocity Genes Scores () element allowing identification of velocity genes driving the dynamics.

The workflow can be found here:

        Template Workflows | Single Cell Workflows () | From Imported Data () | Expression Analysis from Matrix ()

If you are connected to a CLC Server via the CLC Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.

Choose either one or more Expression Matrix () / () or Select files for import and select the formats that are compatible with the selected inputs. Read more about import options in Importing data.

The workflow offers a number of options. Note that not all parameters can be configured. Open parameters indicate places where customization may be necessary for different samples, but default settings are suitable in most cases.

The workflow can be run using Single Cell hg38 (Ensembl) or Single Cell Mouse (Ensembl) reference data sets (see Reference data management).

The workflow allows the analysis of multiple samples and you can specify metadata during workflow execution. This is converted to cell annotations and can be used for coloring the cells in the Dimensionality Reduction Plot. However, the workflow expects each sample to be present in just one Expression Matrix, and attempting to define batch units containing more than one Expression Matrix will lead to a failure during execution.

For more details on configuring workflow execution with metadata, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html. Make sure to inspect the batch overview to check that the analysis will be performed correctly.

For quality control a number of options exist. The option to remove empty droplets is not suitable for protocols that do not use droplets, and removing barcodes with low number of reads or expressed features might be more appropriate. Quality Control (QC) uses the number of reads mapped to the mitochondria, and for this the name of the mitochondria chromosome needs to be provided. The default value is often the correct name. After quality control, the matrices are collected and normalized jointly. Note that batch correction is not performed. Read more about QC and normalization in Gene Expression Matrix.

For clustering and creation of the Dimensionality Reduction Plot plot, it is possible to restrict analysis to highly variable genes. The data is then projected to a lower dimensional space using PCA. You can read about this feature in Feature selection and dimensionality reduction.

Velocity can optionally be calculated by setting "Velocity Analysis" to "Run velocity analysis" in the "Enable Velocity Analysis" wizard step, see Velocity analysis in workflows. Velocity is calculated for each sample individually by default. If "Calculate velocity for each sample independently" is unticked, the velocity is calculated using all cells across samples.

The high confidence predicted cell types ("Cell type (high confidence)") are used to group the cells in the expression plots (Heat Map and Dot Plot) and Cell Abundance Heat Map, as well as for scoring the velocity genes. The Cell Abundance Heat Map additionally groups the cells based on the automated clusters obtained with resolution 1.0 ("Leiden (resolution=1.0)"). Any of these groups can be changed to:

• all predicted cell types ("Cell type (all)");
• automated clusters obtained with a different resolution ("Leiden (resolution=)"). All resolutions are produced, in steps of .

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Subsections

• Output from Expression Analysis from Matrix

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