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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
Reference data management
The Reference Data Manager
Running tools and workflows
Data import
Import Expression Matrix
Import Peak Count Matrix
Import Cell Annotations
Import Cell Clusters
Import Cell Clonotypes
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 Loom Expression Matrix
Export MEX Expression Matrix
Export TXT Expression Matrix
Export Peak Count Matrix
Prepare Reads
Annotate Reads with Cell and UMI
Setting the sample name
Interpreting the output of Annotate Reads with Cell and UMI
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
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
Cell Type Classification
Browse QIAGEN Cell Ontology
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
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
Velocity Analysis
Single Cell Velocity Analysis
Interpreting the output of Single Cell Velocity Analysis
The velocity estimation algorithm
Differential Velocity for Single Cell
Score Velocity Genes
Interpreting the output of Score Velocity Genes
Create Phase Portrait Plot
Chromatin Accessibility
Single Cell ATAC-Seq Analysis
Interpreting 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
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
Interpreting the output of Compare Cell Clonotypes
Convert Clonotypes to Cell Annotations
Cell Annotations for TCR Cell Clonotypes
Cell Annotations for BCR Cell Clonotypes
The Cell Clonotypes element
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
Interpreting the output of Create Heat Map for Cell Abundance
Dimensionality reduction
UMAP for Single Cell
tSNE for Single Cell
Utility tools
Combine Cell Annotations
Combine Cell Clusters
Convert Metadata to Cell Annotations
Add Information to Plot
Update to Common 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
UMAP and tSNE plot 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
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
System requirements and installation
Subsections
System requirements
Installation of modules
Uninstalling modules
