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• Introduction
  • The concept of CLC Single Cell Analysis Module
  • Contact information
  • System requirements and installation
    • System requirements
    • Installation of modules
    • Uninstalling modules
  • Licensing modules
    • Server License
  • The QIAGEN Cell Ontology
  • Reference data management
    • The Reference Data Manager
  • Running tools and workflows
• Data import
  • Import Expression Matrix
  • Import Cell Annotations
  • Import Cell Clusters
  • Import Cell Clonotypes
• Data export
  • Export Cell Ranger HDF5 expression matrix
  • Export Loom expression matrix
  • Export MEX expression matrix
• Creating a count matrix from FASTQ
  • Annotate Reads with Cell and UMI
    • Setting the sample name
    • Interpreting the output of Annotate Reads with Cell and UMI
  • Single Cell RNA-Seq Analysis
    • The Single Cell RNA-Seq Analysis report
    • The Single Cell RNA-Seq Analysis algorithm
• Cell preparation
  • QC for Single Cell
    • Empty droplets filter
    • Count-based and extra-chromosomal filters
    • Doublets filter
    • Interpreting the output of QC for Single Cell
    • Choosing barcodes to retain
    • The cell calling algorithm
    • The doublet calling algorithm
  • Normalize Single Cell Data
    • When is batch correction appropriate?
    • Interpreting the output of Normalize Single Cell Data
    • The Normalize Single Cell Data algorithm
  • Combine Cell Annotations
  • Combine Cell Clusters
  • Convert Metadata to Cell Annotations
  • Update to Common Sample Name
• Noise reduction through feature selection and PCA
  • Feature selection and PCA
    • Calculation of estimated biological variation
• Cell Annotation
  • Predict Cell Types
  • Train Cell Type Classifier
    • Features used for training and prediction
    • Interpreting the output of Train Cell Type Classifier
    • SVMs for cell type classification
  • Cluster Single Cell Data
    • The Cluster Single Cell Data algorithm
  • Create Heat Map for Cell Abundance
    • Interpreting the output of Create Heat Map for Cell Abundance
• Dimensionality reduction
  • Create UMAP Plot
  • Create tSNE Plot
  • Add Information to Plot
• Expression Analysis
  • Differential Expression for Single Cell
    • Interpreting 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
• Immune Repertoire
  • Single Cell Immune Repertoire Analysis
    • The report output from Single Cell Immune Repertoire Analysis
    • The Cell Clonotypes element
    • The clonotype identification algorithm
  • Filter Cell Clonotypes
  • Combine Cell Clonotypes
  • Compare Single Cell Immune Repertoires
    • Interpreting the output of Compare Single Cell Immune Repertoires
  • Convert Clonotypes to Cell Annotations
• Single cell workflows from reads
  • Expression Analysis from Reads
    • Configuring the batch units
    • Output from Expression Analysis from Reads
  • Immune Repertoire Analysis from Reads (10xVDJ)
    • Output from Immune Repertoire Analysis from Reads (10xVDJ)
  • Immune Repertoire and Expression Analysis from Reads (10xVDJ)
    • Configuring the batch units with multiple input types
    • Output from Immune Repertoire and Expression Analysis from Reads (10xVDJ)
• Single cell workflows from imported data
  • Expression Analysis from Matrix
    • Output from Expression Analysis from Matrix
  • Immune Repertoire and Expression Analysis from Clonotypes and Matrix
    • Output from Immune Repertoire and Expression Analysis from Clonotypes and Matrix
• UMAP and tSNE plot functionality
  • Manual Annotation
  • Create Subset
  • Extract to Table
  • Launching of Create Expression Plot
  • Launching of Create Heat Map for Cell Abundance
  • Launching of Differential Expression for Single Cell
• Licensing requirements for the CLC Single Cell Analysis Module
  • Licensing modules on a Workbench
    • Request an evaluation license
    • Download a license using a license order ID
    • Import a license from a file
    • Configure License Server connection
    • Download a static license on a non-networked computer
  • Licensing Server Extensions on a CLC Server
    • Download a static license on a non-networked machine
• Bibliography

Server License

To use the tools and functionalities of CLC Single Cell Analysis Module on a CLC Server:

1. You need to purchase a license for the CLC Single Cell Analysis Server Extension.

2. A server administrator must install the CLC Single Cell Analysis Server Extension license on the single server, or on the master node in a job node or grid node setup, as described in Licensing Server Extensions on a CLC Server.

3. A server administrator must install the CLC Single Cell Analysis Server Extension on the CLC Server, as described below.

Download and install server plugins and server extensions

Plugins, including server extensions (commercial plugins), are installed by going to the Extensions () tab in the web administrative interface of the single server, or the master node of a job node or grid nod setup, and opening the Download Plugins () area (figure 1.5).

Figure 1.5: Installing plugins and server extensions is done in the Download Plugins area under the Extensions tab.

If the machine has access to the external network, plugins can be both downloaded and installed via the CLC Server administrative interface. To do this, locate the plugin in the list under the Download Plugins () area and click on the Download and Install... button.

To download and install multiple plugins at once on a networked machine, check the "Select for download and install" box beside each relevant plugin, and then click on the Download and Install All... button.

If you are working on a machine without access to the external network, server plugin (.cpa) files can be downloaded from: https://digitalinsights.qiagen.com/products-overview/plugins/ and installed by browsing for the downloaded file and clicking on the Install from File... button.

The CLC Server must be restarted to complete the installation or removal of plugins and server extensions. All jobs still in the queue at the time the server is shut down will be dropped and would need to be resubmitted. To minimize the impact on users, the server can be put into Maintenance Mode. In brief: running in Maintenance Mode allows current jobs to run, but no new jobs to be submitted, and users cannot log in. The CLC Server can then be restarted when desired. Each time you install or remove a plugin, you will be offered the opportunity to enter Maintenance Mode. You will also be offered the option to restart the CLC Server. If you choose not to restart when prompted, you can restart later using the option under the Status and Management tab.

For job node setups only:

• Once the master CLC Server is up and running normally, then restart each job node CLC Server so that the plugin is ready to run on each node. This is handled for you if you restart the server using the functionality under the Server Maintenance area under the Admin () tab.
• In the web administrative interface on the master CLC Server, check that the plugin is enabled for each job node.

Installation and updating of plugins on connected job nodes requires that direct data transfer from client systems has been enabled. See Direct data transfer from client systems for details.

Grid workers will be re-deployed when a plugin is installed on the master server. Thus, no further action is needed to enable the newly installed plugin to be used on grid nodes.

Links to related documentation

• Logging into the CLC Server web administrative interface: http://resources.qiagenbioinformatics.com/manuals/clcgenomicsserver/current/admin/index.php?manual=Logging_into_administrative_interface.html

• Maintenance Mode: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Server_maintenance.html
• Restarting the server: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Starting_stopping_server.html
• Plugins on job node setups: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Installing_Server_plugins_on_job_nodes.html
• Grid worker re-deployment: https://resources.qiagenbioinformatics.com/manuals/clcserver/current/admin/index.php?manual=Overview_Model_II.html

Managing installed server plugins and server extensions

Installed plugins are managed and can be uninstalled from under the Manage Plugins () area figure 1.6 of the Extensions () tab.

As when installing plugins, the CLC Server must be restarted to complete the action. See above for links to further information.

The list of tools delivered with a server plugin can be seen by clicking on the Plugin contents link to expand that section. Workflows delivered with a server plugin are not shown in this listing.

Figure 1.6: Managing installed plugins and server extensions is done in the Manage Plugins area under the Extensions tab. Clicking on Plugin contents opens a list of the tools delivered by the plugin.

Plugin compatibility with the server software

The version of plugins and server extensions installed must be compatible with the version of the CLC Server being run. A message is written under an installed plugin's name if it is not compatible with the version of the CLC Server software running.

When upgrading to a new major version of the CLC Server, all plugins will need to be updated. This means removing the old version and installing a new version.

Incompatibilities can also arise when updating to a new bug fix or minor feature release of the CLC Server. We recommend opening the Manage Plugins area after any server software upgrade to check for messages about the installed plugins.

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Server extension licensing

Commercial plugins, known as server extensions, require a license to be installed in the CLC Server before analysis tools delivered by the extension can be used. The license only needs to be present on the master server on grid and job node setups^1.1. If a license file is present, but it is valid only for an older version of the plugin, or it has expired, a warning will be shown.

Please refer to the appendix of the individual commercial plugin manuals for detailed information about licensing of that product.

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Footnotes

... setups^1.1

Prior to CLC Genomics Server 11.0, module licenses were also required on nodes.

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