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Statistical inference and Summary charts
Statistical Inference and Summary charts
Getting Started
About Cytobank
- Common Troubleshooting
- Cytobank frequent asked questions (FAQs)
- What is Cytobank?
- The Differences between Basic Cytobank, Premium Cytobank, and Enterprise Cytobank
- How to get help or support for Cytobank
- Minimum System and Software Requirements for Cytobank
Account Basics
Security
Cytobank Essentials: Core Overviews
Cytobank Core Overview Articles
- Introduction to the machine learning tools in the Cytobank platform
- Overview of linked experiments
- Overview of uploading data to Cytobank
- Overview of Cytobank anatomy and organization, basic concepts
- Overview of the Experiment Manager
- Overview of Gating in Cytobank
Gating
Articles on Gating
- Overview of Gating in Cytobank
- Choose a compensation on which to draw a gate
- The Difference Between a Gate and a Population: Using the Population Manager and considerations for deleting and renaming gates
- Hidden gates: a gate is tied to a compensation, channel selection, and scale settings, and is visible only when they are set accordingly
- The "Apply" and "Apply and Return" buttons and gate versioning
- Seeing gate location across all files in the experiment (Check Gates functionality)
Gating-based Visualizations
Sample Tags and Annotating Scientific Variables
Articles
Panels, Channels, and File Categorizations
Figures (Illustrations)
Articles
- Understanding the Illustration Editor and Saved Illustrations
- Download or export plots and figures as images, SVG, and PDF
- How to create and configure a Heatmap
- Statistics and fold change equations in the Illustration Editior
- How to export and download Statistical Inference and statistical table from an Illustration
- Dot Plots Colored by Channel
Advanced Analysis - SPADE, FlowSOM, viSNE, and CITRUS
Articles on FlowSOM
Articles on SPADE
- Overview and introduction to SPADE
- How to Configure and Run a SPADE Analysis
- SPADE with fold change: overview, setup, and analysis
- Analysis and Interpretation of SPADE Results
- SPADE metrics: Median, Raw Median, Fold, Raw Fold, and CV
- Export images of a SPADE tree
Articles on Dimensionality Reduction Suite
- The effect of dimensionality reduction settings on run time
- Introduction to the dimensionality reduction suite in the Cytobank platform
- Comparison of the dimensionality reduction results within the Settings page
- How to configure and run a dimensionality reduction analysis
- Analysis and interpretation of the dimensionality reduction (DR) results
- How to concatenate dimensionality reduction files for analysis
Articles on CITRUS
Data Scaling and Transformation
Articles
Compensation
Articles on Compensation
- How the experiment-wide compensation works in Cytobank
- Import a compensation matrix from a CSV file into Cytobank
- Working in Cytobank with data compensated in a different software
- Create a compensation matrix automatically from single stain controls (automatic compensation)
- Import an existing compensation matrix from another Cytobank experiment
- Modify a File-Internal Compensation matrix in Cytobank (import a compensation matrix from an FCS file)
Exporting Data and Statistics
Articles on Exports
- Statistics in Cytobank: Percent of Population, Percent in Gate, and Event Count Ratio
- Export data as FCS or spreadsheet files from whole files and/or gated populations
- Download FCS files and other files from Cytobank
- Download and transfer an entire Experiment and analyses between Cytobanks as an ACS file
- Exporting a spreadsheet of batched statistics using the Export statistics tool (for import into Prism, Spotfire, Excel, Tableau, etc.)
Data Management, Sharing, Collaboration, and Permissions
Articles on Data Sharing
Articles on Data Management
- Upload fresh data to Cytobank
- Clone an experiment to make a copy for your own use
- The Experiment summary page
- The FCS file details page
- Warnings on FCS files: Understanding the Cytobank File QC system
- Delete an experiment
Publishing on Cytobank
FAQ
The Cytobank API
Articles on the Cytobank API
Workflows Using the Cytobank API
Templated Analysis
Analysis Templates Articles
- Compensation templates
- Sharing statistics templates
- Illustration settings templates
- Illustration/figure templates: transfer saved illustrations between experiments (import illustrations)
- Sample Tags templates
- Gating templates
Misc
Articles
- Finding IDs in Cytobank via the URL Bar
- Dedicated Asynchronous Compute Tasks
- How to reference Cytobank when publishing
- How to open and use your browser's JavaScript console
- Analyze Other Data Types in Cytobank by Conversion to FCS with DROP
- Using keyboard hotkeys