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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

Other formats

MEX importer

This importer requires the following files to be supplied:

• Barcodes file. A file with the extension .tsv, conventionally barcodes.tsv. It contains tab-separated columns, and has one row per barcode. It can optionally contain a header. The barcodes are read from the first column. Empty lines are ignored.

  Use the Cell format option to control how the barcodes should be interpreted - for example if it also includes information about the sample.

• Feature file. A file with the extension .tsv, conventionally features.tsv or genes.tsv. It contains one row per feature. It can optionally contain a header. Empty lines are ignored.

  It contains multiple tab-separated columns:

  • One column: the feature name.
  • Two columns: the feature identifier and name.
  • Three columns: the feature identifier, name, and type. Of the commonly used feature types, "Gene Expression", "Transcript Expression", and "Spike-in" are the most important ones. Other features, such as "Antibody Capture" will be silently ignored by most tools.

  For 10x Multiome files there will be six columns. The last three consist of genome coordinates and will be ignored. Lines with feature type "Peaks" will also be ignored. They should instead be imported as a Peak Count Matrix (see Import Peak Count Matrix).

• Matrix file(s). File(s) with the extension .mtx in the Matrix Market Exchange Coordinate Format, see https://math.nist.gov/MatrixMarket/formats.html for details. Features must be in the first dimension (rows) and cells in the second (columns).

  Expressions and/or spliced and unspliced counts can be imported using:

  • Matrix file for expressions, conventionally named matrix.mtx.
  • Matrix file (spliced) for spliced counts, conventionally named spliced.mtx.
  • Matrix file (unspliced) for unspliced counts, conventionally named unspliced.mtx.

  See Options for importing spliced and unspliced counts for more details.

Additional options are:

• Name. The name of the imported matrix. If Cell format is not configured to parse a sample name from each barcode in the barcodes file, then this will also be the sample name for all the imported barcodes.
• Files are in same directory. This option is provided for convenience and works for local files. When checked, if any file option is updated to a file in a new directory, the other files are automatically updated, if files with the conventional names can be found in the directory.

MEX archive importer

The MEX archive importer is provided for convenience. A .zip, .tar or .tar.gz archive file can be provided in the Archive file containing the files required by the MEX importer. In order to uniquely identify each file, these must have a specific name:

• Barcodes file must be named barcodes.tsv
• Feature file must either be named features.tsv or genes.tsv
• Matrix file must be named matrix.mtx
• Matrix file (spliced) must be named spliced.mtx
• Matrix file (unspliced) must be named unspliced.mtx

The importer can be configured to either import an Expression Matrix (), or an Expression Matrix with spliced and unspliced counts (). For the first option, `Import expressions' must be enabled, while for the second option, `Import spliced/unspliced' must be enabled.

Either the `Matrix file', or `Matrix file (spliced)' and Matrix file (unspliced)' can be missing from the archive, depending on how the importer has been configured.

For all three .mtx files, the features must be in the first dimension (rows) and cells in the second (columns). See https://math.nist.gov/MatrixMarket/formats.html for details of the Matrix Market Exchange Coordinate Format.

See Options for importing spliced and unspliced counts for more details on how the total expression is calculated.

Parse Bio MTX importer

This importer requires three files to be supplied:

• Cell metadata file. A file with the extension .csv and comma separated columns, with one row per barcode. It must contain headers. The following options relating to the cell metadata file are available:
  • Barcode column. The name of the column containing the barcodes.
  • Cell metadata has sample name. If checked, the sample name is read from the file. Otherwise, the sample name is defined by the general options (see Cell format in importers).
  • Sample column (Optional). The name of the column containing the sample names.

• Feature file. A file with the extension .csv and comma separated columns, with one row per feature. The following options relating to the feature file are available:
  • Feature id column (Optional). The name of the column containing the feature identifiers (e.g., ENSG00000243485 for ENSEMBL).
  • Feature name column.The name of the column containing the feature names.

• Matrix file. A file containing the expression with the extension .mtx in the Matrix Market Exchange Coordinate Format. Cells must be in the first dimension (rows) and features in the second (columns). See https://math.nist.gov/MatrixMarket/formats.html for details of the Matrix Market Exchange Coordinate Format.

Plain Text Table importer

This importer supports import of text data in a full plain text table format.

• Expression matrix. A single file to be imported.
• Table layout. Choose whether the table has cells in columns and features in rows, or is transposed such that features are in columns and cells are in rows.
• Separator. Choose the column separator.

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