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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 Cell Annotations
Import Cell Clusters
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
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
Interpreting the output of QC for Single Cell
Choosing barcodes to retain
The cell 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
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
Interpreting the output of Train Cell Type Classifier
Features used for training and prediction
SVMs for cell type classification
Cluster Single Cell Data
The Cluster Single Cell Data algorithm
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
Create Expression Plot
The Heat Map output of Create Expression Plot
The Dot Plot output of Create Expression Plot
Single cell workflows
Perform Single Cell Analysis from Expression Matrix
Output from Perform Single Cell Analysis from Expression Matrix
Perform Single Cell Analysis from Reads
Configuring the batch units
Output from Perform Single Cell Analysis from Reads
UMAP and tSNE plot functionality
Manual Annotation
Create Subset
Extract to Table
Launching of Create Expression Plot
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
Dimensionality reduction
Subsections
Create UMAP Plot
Create tSNE Plot
Add Information to Plot