CytoAnalyst!
What is CytoAnalyst?
CytoAnalyst is a web-based application for the analysis of single-cell RNA-seq data. It provides a user-friendly interface to perform quality control, data visualization, and various types of analyses.
Key Features
Interactive visualizations: A wide range of interactive visualizations to explore single-cell data, including scatter plots, heatmaps, dot plots, and violin plots with support for multiple blending modes
Flexible data import: Support for multiple data formats including AnnData and 10x Genomics
Quality control: Built-in QC metrics and filtering capabilities
Data analysis tools: Comprehensive suite of analysis methods including:
Embedding analysis and visualization
Clustering and subclustering
Differential expression analysis
Cell type annotation and prediction
Pseudotime trajectory inference
Gene set enrichment analysis
Collaborative features: Share studies with colleagues and control access permissions
System Requirements
Browser: CytoAnalyst is a web-based application and can be accessed using modern web browsers such as Google Chrome, Mozilla Firefox, or Safari.
About this Documentation
This documentation provides a comprehensive guide to using CytoAnalyst for the analysis of single-cell RNA-seq data.
Main Topics
Getting Started
Getting Started: Get familiar with the CytoAnalyst interface using a sample dataset
Study Management: Create, edit, delete, and share studies
Data Management: Import and filter single-cell data
Data Analysis: Overview of the analysis interface and tools
Core Analysis Features
Data Visualization: Interactive visualization tools and customization options
Embedding Analysis: Dimension reduction and visualization
Clustering Analysis: Cell clustering and analysis
Differential Expression Analysis: Compare gene expression between groups
Cell Annotation: Annotate cells and manage cell metadata
Gene Set Collection: Create and manage gene sets
Enrichment Analysis: Analyze gene set enrichment
Pseudotime Trajectory: Infer cellular trajectories
Additional Features
Cell Filtering: Filter cells based on various criteria
Study Logs: Monitor analysis jobs and system status