How to Use
This tutorial aims to guide you on how to use CellAnalyst software to help you conduct your research more efficiently.
Load the Project
After exporting the required files using ExportToCellAnalyst.R, you can import the dataset into CellAnalyst on the Browse page.
① Navigate to the Browse Page
Start by clicking the "Browse" button in the top menu.
② Enter Project Details
In the Load Project section, fill in the species (e.g., human) and the corresponding Project ID (e.g., E-MTAB-7407_P01).
③ Select the Project Directory
Click on the "Choose Files" button to select the project directory generated by the R script (ExportToCellAnalyst.R).
④ Upload Files
Confirm the file selection in the pop-up window by clicking the "Upload" button.
⑤ Import the Data
Initiate the import process by clicking the "Import" button.
⑥ Project Confirmation
Once uploaded and imported, the new project will appear in the main view. Click to browse the project in the main scope view.
The Main Embedding Module
The embedding module offers an interactive way to explore your single-cell dataset through a dynamic scatter plot.
① Interactive Scatter Plot
The main scatter plot displays cells as individual points, with colors assigned based on a chosen metadata attribute (such as cell type).
② On-Demand Details
Hover over any cell to reveal its specific metadata details, enabling deeper insight into individual cell characteristics.
③ Cluster Isolation
Double-click on a cluster to highlight or isolate that group, and double-click again to revert to the full view.
④ Comparative Insights
An optional split view allows you to segregate the data by another metadata category, helping to compare different conditions or time points side-by-side.
The Function Visualization Module
The Overview Panel
This panel shows the cell composition and cell quality metrics of the single-cell dataset.
Cell Composition
It displays a bar chart that breaks down the sample into its various cell types. This visual helps identify the distribution and the relative abundance of different cell populations within the sample.
① Metadata Grouping
Select a metadata category (e.g., cell type) using the dropdown menu to visualize the overall composition of your cells.
② Interactive Details
Hover over each segment in the horizontal bar chart to reveal detailed information about the corresponding cell type and its proportion.
③ Comparative Analysis
Optionally, use a secondary dropdown to further split the data based on another metadata attribute, which updates the view with additional bar charts for comparison, such as across different time points.
Cell Quality
This section shows a violin plot that represents the distribution of a quality metric. It is used to assess and compare the quality of data across different groups.
① Select Quality Metrics
Evaluate data integrity by selecting a quality control metric (e.g., nFeature_RNA) to assess how robustly your data is captured.
② Interactive Details
Hover over the plots to reveal detailed information, enabling you to quickly identify patterns or potential quality issues within specific groups.
③ Grouped Violin Plots
View interactive violin plots that display the distribution of the chosen metric across different groups, such as samples or developmental stages.
The Marker Dots Panel
This dot plot displays gene expression across multiple cell types. Genes are arranged on one axis and cell types on the other. Each dot’s size and color intensity indicate the level of expression, with larger and more vividly colored dots representing higher expression levels.
① Adjust Marker Number
The plot represents each cell type-marker gene pair with a dot (determined by COSG). Its size indicates the average expression level (AvgExpr), while its color intensity reflects the percentage of cells expressing the gene (PerExpr). You can select the number of top marker genes for display to focus on the most informative markers per cell type.
② Interactive Details
Hover over any dot to reveal precise expression details for an in-depth assessment of cell type-specific gene expression profiles.
The Expression Panel
This panel illustrates gene expression on the embedding plot or violin plot.
Plot with Embedding
① Expression on Embedding
The feature plot displays cells in an embedding, coloring them based on the expression level of a user-specified gene, which helps reveal spatial patterns.
② Interactive Details
Hover over individual cells to see details such as cell barcode, cell type, expression values, and spatial coordinates.
③ Customizable Metadata Splitting
Refine the view by splitting the data based on selected metadata, enabling comparisons across different groups or time points.
Plot with Violin
① Gene-Specific Visualization
Enter a gene of interest to display its expression distribution using violin plots, providing a clear view of variability across cell types.
② Metadata-Based Splitting
Tailor the analysis by splitting the violin plots according to a selected metadata column, allowing for comparisons across different conditions or time points.
③ Interactive Details
Hover over the plots to access detailed expression information for each cell type, facilitating a more in-depth interpretation of the dataset.
The Enrichment Panel
① Cell Type-Specific Analysis
Select a cell type to focus on the enrichment of genes that are particularly characteristic of that population.
② Top Term Customization
Adjust the number of top enriched terms displayed to control the level of detail and maintain a clear overview of your functional analysis.
③ Interactive Details
Explore the enrichment results with interactive dot plots where hovering over each dot reveals detailed information such as term descriptions, significance values, gene counts, and the associated gene list.
The Meta Table Module
This module displays the marker gene table and cell metadata for each single-cell dataset.
Marker List with Dots
① Adjustable Pagination
Easily control the number of rows displayed per page for streamlined browsing of the marker gene list.
② Cell Type Selection
Choose a specific cell type to dynamically update and display its corresponding marker genes along with essential statistics.
③ Interactive Details
Hover over any gene to reveal detailed metrics such as cluster information, average expression, and the percentage of cells expressing the gene.
④ Search Functionality
Quickly locate specific genes by entering your query in the search bar.
Cell Meta Table
① Customizable Pagination
Adjust the number of rows displayed per page using a dropdown menu for tailored browsing.
② Interactive Search
Use the search box to quickly filter and pinpoint specific cells based on any metadata.