Statistical inference and Summary charts

Statistical Inference and Summary charts

• How to set up a paired statistical test
• Overview of statistical inference method
• Overview of Summary plots generation using the Illustration Editor
• How to create stain index charts for antibody titration

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

• Register an account with Cytobank, get validated, and verify your Email
• Password Reset
• Converting from OpenID to Password Based Login

Security

• Overview of data security, integrity, and backup on Cytobank
• Storing clinical data on Cytobank (HIPAA, 21 CFR Part 11)

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

See all 9 articles

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)

See all 14 articles

Gating-based Visualizations

• Automatically Generated Figure of Gating Strategy
• Population Tree
• Population Sunburst

Sample Tags and Annotating Scientific Variables

Articles

• How to annotate data with sample tags in Cytobank (tutorial)
• Annotate data during collection for efficient transfer to Sample Tags in Cytobank
• Import Sample tags from an existing Cytobank experiment
• Exporting and importing Sample tags: annotate files by spreadsheet

Panels, Channels, and File Categorizations

• Overview of working with panels and channels
• Categorizing files as Experiment Files, Compensation Controls, and Other Controls
• How to resolve panels with channel conflicts

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

See all 15 articles

Advanced Analysis - SPADE, FlowSOM, viSNE, and CITRUS

Articles on FlowSOM

• Introduction to FlowSOM in Cytobank
• How to Configure and Run a FlowSOM Analysis
• Analysis and Interpretation of FlowSOM Results
• The Effect of FlowSOM Settings on Run Time
• FlowSOM FAQ

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

See all 11 articles

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

See all 9 articles

Articles on CITRUS

• Overview of CITRUS
• How to Configure and Run a CITRUS Analysis
• Analysis and Intepretation of CITRUS Results
• Exporting Clusters from a CITRUS Analysis as New FCS Files

Data Scaling and Transformation

Articles

• About the Arcsinh transform
• Scale types and equations in Cytobank
• View and adjust scale type, maximum, minimum, and scale argument for a channel

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)

See all 7 articles

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

• Use projects to share data, collaborate with a group, and set custom access permissions
• Sharing data with Cytobank subscribers across different Cytobanks

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

• Setting up a public page on Cytobank for your lab

FAQ

• Can data be accessed after a paid or trial subscription expires? Are data deleted? How to transfer data after a license expires?
• How to delete FCS files from an Experiment
• Is there a limit or maximum amount of data that I can upload to Cytobank?

The Cytobank API

Articles on the Cytobank API

• Overview of the Cytobank API
• Cytobank API endpoint documentation
• Cytobank API Libraries for Programming Languages
• Generate an API token in Cytobank
• Using R to Interface with Cytobank Prerequisites

Workflows Using the Cytobank API

• Workflows using the Cytobank API
• CytobankBridgeR Guide

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

See all 7 articles

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

See all 9 articles

Cytobank Utilities

• FCS file concatenation tool